The evangelical Christian charity which led the legal action against the Scottish government on the controversial Named Person legislation is to be investigated over whether it misused funds in pursuing the case.

The Christian Institute, a creationist charity which believes that every word in the bible is fact, joined with other conservative and religious charities, and three individuals, in an effort to stop the Scottish government introducing the nation-wide welfare scheme for all children. Their appeal against it was successful in the Supreme Court on Thursday after it had been dismissed by the Court of Session in Edinburgh last year.

The Charity Commission, which governs charities, will now have to decide whether the Christian Institute's spending on the case, and that of its three other charity partners, was a justified use of funds. There are strict rules concerning political campaigning and spending, which is only permitted when it is in pursuit of the charity’s aims and objectives. The institute has been criticised in the past by the commission for inappropriate campaigning.

The Christian Institute and the other groups who took the legal action - including the Family Education Trust and CARE, Christian Action Research and Education - also came together to form the campaigning group No To Named Person, or NO2NP. According to the group’s website more than 35,000 people have signed a petition against the scheme. Under it a mentor, usually a teacher, is responsible for the well-being of the child and has access to a wide range of information.

In court in London the Scottish government was told to go back and think again. The five judges ruled that while the provision of the 2014 the Children and Young People Act was 'unquestionably legitimate and benign' it breached Article 8 of the European Convention on Human Rights, the right to a private and family life. The court was concerned about how private information was shared and who had access to it. The government was given six weeks to come back with amended proposals.

The case has so far cost around £300,000, and is likely to rise to £500,000, which the institute and the other charities have underwritten.

Simon Calvert is the deputy director of the Christian Institute and also the spokesman for NO2NP. Despite several requests he did not respond to our inquiries.

According to the charity's latest accounts, income for the year 2014 was more than £2.6m. It is based in Newcastle and has more than 50 employees, according to the return.

It has previously campaigned against gambling, abortion and euthanasia but most vigorously against homosexuality. It sought to raise the age of consent for gay people, it opposed civil partnerships and same sex marriages as well as legislation to allow gay couples to adopt. As a charity it has been censured by the Charity Commission for breaching rules on overt political campaigning. Most notoriously it produced an organ-donor style plastic card that read: "In the event of my death, I do not want my children to be adopted by homosexuals".

The charity also has a history of funding defendants accused of discriminating against gay people. In May 2008 it funded the legal costs of Lillian Ladele, a registrar in Islington against her council employer, after she was disciplined for refusing, on religious grounds, to process paperwork associated with civil partnerships. The case was lost.

In 2010 the institute paid the defence of two Christian hoteliers accused under the Equality Act after they had refused to allow a gay couple in a civil partnership to stay in a double room. Once more they lost.

The CI is also funding the appeal by the family which owns Ashers Baking Company in Belfast. They were convicted because they refused to decorate a cake saying Support Gay Marriage for a male couple's wedding. The appeal judgement is still being considered.

John Swinney, the deputy first minister, has insisted that Named Person will go ahead. It is likely that a compromise will be taken back to the court, similar to the requirements of data protection legislation where a person has the right – in this case a parent – to know who the named person is and what information is being held, with the ability to question or correct wrong information.

Despite the SNP government’s embarrassment over being forced to remodel the legislation there is still a Holyrood majority for the plan and it is backed by frontline services like Barnardo's and health visitors.

The original act which contains the provision was passed without a single vote against it. The Tories abstained but two years later its scrapping became a key plank in their election manifesto. Leader Ruth Davidson hit out saying, “the SNP does not know better than parents when it comes to raising their children.”

Labour also backed the plan but midway through last May's election reversed their support and called for a review of the “absolute mess” they had previously voted for.

The scheme is already being piloted in several Scottish local authority areas, including Edinburgh and Fife.

NO2NP waded into the controversy over the murder of two-year-old Liam Fee by questioning whether the scheme had obstructed targeted intervention. The child was battered to death in 2014 by his mother Rachel and her partner Nyomi Fee.

The scheme was meant to have been implemented across the country by August 31. Despite the court setback the Government is still hoping to have it running in every area before the end of the year.

Deputy First Minister John Swinney reiterated that the Government remains committed to it. He said: "I have already spoken directly with senior figures from the public and third sectors including NHS, local authorities and Police Scotland to discuss our next steps."

Simon Calvert, who is NO2NP spokesman as well as deputy director of the Christian Institute, responded: "We have had to drag Government and their supporters through the courts to prove what we have been saying for two years was correct and that the named person scheme as enacted is illegal.

"People have the right to request copies of any personal information an organisation may be holding about them through a Subject Access Request." He added: "All the information which has been gathered in recent years should be handed over to families and any data which is held by public bodies should be removed and destroyed."