Ian Taylor's Vitol international trading group also avoided UK tax and has been linked to dubious deals in Serbia, Iraq, Iran and Libya.
Mr Taylor is president and chief executive of Vitol.
It was founded in Rotterdam, operates out of London but headquartered in Switzerland, which has allowed it to sidestep European Union rules on issues such as sanctions.
The SNP said the claims against Better Together's chief donor and his firm were "serious and raised urgent questions" the No campaign must answer.
A Better Together spokesman said: "This was a donation from a private individual. It was given and received in good faith."
Mr Taylor's donations to the Conservative party have already been criticised by Labour, casting doubt on how appropriate they are for all-party Better Together.
Proud of his Scots family roots but raised and educated in England, Mr Taylor spoke of his pride at putting more than £500,000 into the No campaign, saying at the weekend he had been "delighted to help".
He moved from Shell to Vitol in 1985 and became chief executive 10 years later. While at the helm, Vitol, the world's largest oil trading company, has been involved in a number of controversies.
l In 2001, The Observer revealed the firm paid £1 million to Serbian war criminal Arkan to sort out an oil deal with the regime of Slobodan Milosevic which had turned sour. Vitol said no illegal conduct was involved in this transaction.
l In 2007, Vitol pled guilty in a New York court to paying surcharges to Iraq's national oil company during Saddam Hussein's regime, undermining the UN oil-for-food programme in Iraq. It paid fines, restitution and costs totalling $17.5m.
l In September last year, Vitol admitted buying and selling Iranian oil in a deal with China, but its Swiss status meant it did not breach EU and US sanctions. Vitol has confirmed it has since ended all sales of oil to and from Iran and has not broken any trading sanctions.
l During and after the Libyan conflict, Vitol played a controversial role, providing fuel to rebels and selling their raw product. These deals were said to have involved Foreign Office officials and International Development Minister Alan Duncan – a former friend and work colleague of Mr Taylor and the recipient of donations from him.
l Last year, it was revealed that for a decade the company had been using Employee Benefit Trusts which avoided tax on incomes of its UK staff and was in discussion with HMRC about a deal to pay this off.
l Mr Taylor, said to have donated more than £500,000 to the Tories, became a member of David Cameron's Leaders' Club, entitling him to attend a dinner at No 10 Downing Street in November 2011. It was claimed the £500m Libyan deal or Mr Duncan's role in it were not discussed.
SNP Westminster leader Angus Robertson said: "This information is extremely serious and raises questions the No campaign must answer. Material in the public domain states that during his tenure as chief executive Mr Taylor's company paid $1m to Serbian war criminal Arkan, who was indicted at the Hague for crimes against humanity."
He said Arkan's crimes of ethnic cleansing were documented as far back as 2001, and included the massacre of 250 patients and staff in a hospital.
Mr Robertson added: "Also during Mr Taylor's tenure it is reported Vitol paid kickbacks to Saddam Hussein's regime in return for oil supply contracts, and was involved in a tax avoidance scheme in the UK for over a decade.
"His donations to the Tories were questioned and criticised by Labour's Douglas Alexander in relation to a conflict of interest about oil contracts in Libya, so the No campaign must have been aware of these matters."
Here are the detailed responses from Vitol to points put by The Herald for this story, which were sent by the company's PR firm at 7pm on April 9 2013, and added online on April 16:
1. (The Herald) In 2001 the Observer revealed that the company paid a million dollars to Serbian war criminal Arkan to sort out an oil deal with the regime of Slobodan Milosevic which had turned sour.
(Vitol) The facts to which the article in question relates date back to the 1990s and did not involve any illegal conduct on Vitol's part. At no stage has any government orregulatory agency investigated or accused Vitol of engaging in any illegal conduct in relation to the facts in question.
2. In 2007 Vitol pleaded guilty in a New York court to paying bribes to officials of Saddam Hussein, undermining the UN oil-for-food programme in Iraq. It paid fines, restitution and costs totalling $17.5m.
This statement is false and misleading. Vitol has never admitted to bribing Iraqi officials and did not plead guilty to paying kickbacks to Iraqi officials under Saddam Hussein's regime. Along with other lifters of Iraqi crude oil under Iraq oil-for-food programme, including some major oil companies, Vitol has acknowledged that some payments were made outside the scope of the UN oil for food programme to the account of the national Iraqi oil company for the development of Iraq’s oil infrastructure. These payments were surcharges demanded by the state oil company of Iraq (SOMO) from all lifters, and were paid to the account of the national Iraqi oil company. They were neither bribes nor kickbacks.
3. In September last year Vitol admitted buying and selling Iranian oil in a deal with China, but its Swiss status meant it did not technically breach EU and US sanctions.
Vitol has at no stage broken any sanctions on trading oil. Vitol ceased all sales of refined product to Iran and all purchases of crude oil from Iran before the introduction of all relevant international legislation. Vitol is fully compliant with applicable international laws and regulations governing trade with Iran. We refer you to a statement published on the Vitol website on 26 September 2012 in this regard:
4. During and after the Libyan conflict Vitol played a controversial role, providing fuel to rebels and selling their raw product – deals said to be brokered by Foreign Office officials and by International Development Minister Alan Duncan – a former friend and work colleague of Mr Taylor and the recipient of donations from him.
The facts are that Vitol and other companies, including various oil majors, were approached by the Qatar International Petroleum Marketing Company Ltd with a request to sell a cargo of crude oil supplied by the Libyan company AGOCO, on behalf of what was then the National Transitional Council of Libya (the ‘NTC’), and in exchange supply AGOCO with oil products for essential power generation and transportation needs. Following detailed negotiations, Vitol agreed to the proposal at very considerable commercial risk.
Neither Mr Duncan, nor the Foreign Office brokered the transactions in question.
5. Last year it was revealed that for a decade the company had been using Employee Benefit Trusts to avoid tax on incomes of its UK staff and was now in discussion with HMRC about a deal to pay this off.
Vitol is satisfied that all its tax affairs are compliant with the appropriate legislation. It does not provide public comment in relation to its dealings with the tax authorities in any of the jurisdictions in which it operates. Nor does it comment on the remuneration of its employees.