THE independence referendum will be tainted if SNP ministers disregard Electoral Commission advice on the rules, Scottish Secretary Michael Moore will warn today.

He will use a speech to the LibDems' autumn conference in Dunfermline to hit back at SNP ministers who have threatened to defy the politically neutral watchdog, which has been handed a key role advising the Government in the run-up to the vote. Mr Moore will say: "There is no other body with the experience and neutrality of the Electoral Commission. To over-rule its judgment would invite the charge of rigging and bias – tainting the process.

"So while every UK government has had the power to do so, none ever has."

Mr Moore negotiated the Edinburgh Agreement paving the way for the referendum – which requires the Scottish Government to consult the Electoral Commission on issues including the wording of the question and campaign funding – with Deputy First Minister Nicola Sturgeon.

In a direct message to her he will say: "The agreement reached between the two governments states that 'the referendum should meet the highest standards of fairness, transparency and propriety, informed by consultation and independent expert advice'.

"Those words were negotiated by the Deputy First Minister. When she publishes the Referendum Bill, with the world watching, Scotland will hold her to them."

Ms Sturgeon last week threatened to defy the Electoral Commission over campaign funding, claiming plans put forward by the watchdog would give the pro-UK parties a combined £1 million advantage.

The SNP again asserted its right to ignore the commission yesterday.

Nationalist MSP Stewart Maxwell – a member of the new Holyrood committee which will scrutinise the Referendum Bill – said: "The anti-independence campaign are guilty of complete hypocrisy. It is they who want to 'rig' the referendum rules to allow the anti-independence camp to massively outspend the pro-independence campaign."

The SNP Government want the two main campaign groups, Yes Scotland and Better Together, to be allowed to spend up to £750,000 each in the final 16 weeks of the campaign.

On top of that, political parties would be allowed to spend up to £250,000, with smaller limits for other organisations and individuals.

The Electoral Commission has suggested the cap for the main organisations should be nearer to £1.5m. It said the parties' spending limits should be based on their share of the vote at the last election.

The row came as Holyrood's new Referendum Committee issued a formal call for evidence on the details of the Edinburgh Agreement.

MSPs are due to consider views on November 15.