The Prime Minister survived the vote by 288 to 97 after he agreed to backtrack on plans to change the purdah rules which normally apply to all elections and prevent ministers using government offices or civil servants to help in a campaign in the month before a vote.
However, in a sign of discontent on the backbenches, the government did suffer its first European rebellion with 25 Tory backbenchers voting for an amendment by leading eurosceptic Sir Bill Cash which would have changed the bill to bring in a normal period of purdah.
And the government was only spared defeat by all but four of Labour’s 256 MPs abstaining, giving Mr Cameron a 191 majority.
Mr Cameron had previously claimed that the experience of the Scottish independence referendum campaign had led him to not want a period of purdah because it had limited his and the UK Government’s role in defending the UK.
And for the second day running, the SNP’s 56 MPs trooped into the lobbies with right-wing Tory rebels to support Mr Cash’s motion, after on Monday backing an amendment by Sir Edward Leigh to give Scotland full fiscal autonomy.
With a rebellion expected, Europe minister David Lidington wrote to MPs promising that the government would bring changes to the next stage of the bill to ensure purdah.
He also made a concession to prevent the referendum being held on the same day as the Holyrood election next year after an amendment tabled by the SNP, which would have blocked the move, looked set to succeed.
But an SNP attempt for “a quad lock” – to ensure the UK could not leave the EU without a majority in all four nations – failed.
Answering the debate, Mr Lidington gave assurances on purdah, pledging the government would not be a “lead campaigner” in the referendum and promising they would bring amendments at the report stage of the bill later this year.
He addressed section 125 of the Political Parties, Elections and Referendums Act 2000 which sets out restrictions on the use of promotional material and campaigning by central and local government.
He said: “The government does need to be free to respond in the national interest and conduct ordinary day-to-day EU business.
“We also believe it would be inappropriate because the referendum is taking place as a result of a clear manifesto commitment to negotiate the terms of the UK’s relationship with the European Union and put them to people in a referendum.”
Despite the government’s efforts, the assurances on purdah did not satisfy all the Tory backbenchers.
Sir Bill dismissed the government’s promise, saying the issue raised a question of trust, and that suspending purdah would be “unfair on the voters” and a “retrograde step” for democracy.
He said: “The problem that we’ve got here is that this situation we’re in now is not necessary and I speak more in sorrow than anger about this.
“I have spoken to the minister for Europe and we’ve had a good discussion as we always do and I was grateful for the fact that he did mention in his own letter that he was grateful for the constructive way in which these concerns were raised.
“But I have to say they haven’t allayed those concerns.”
Tory Bernard Jenkin – who as chairman of the public administration committee in the last parliament carried out an inquiry into whether UK and Scottish Government civil servants abused their position in the independence referendum – said: “This is not about Europe, it is about how to conduct a fair referendum.”
He added: “The machinery of government cannot be involved in supporting one side or the other of a referendum campaign. There are certain myths about this: government doesn’t grind to a halt during a general election; ministers even attend council of ministers meetings during general elections.”
Meanwhile, Tory former cabinet minister Liam Fox also warned that if voters feel the referendum is rigged because the government has used taxpayers’ money to support one side of the debate, the consequences would be “intense”.
Conservative Jacob Rees-Mogg said the government’s ability to influence both the media and the public was considerable.
He added: “Whichever side of the argument one falls on, it must be right to hope that the referendum will be more than just a staging post in the discussion about Europe.”
Speaking for the SNP, Alex Salmond said the events in last year’s referendum demonstrated ministerial promises not to officially interfere would ring hollow.
Reflecting his own anger over the last weeks of the independence referendum, he told the Commons: “Let’s take a scenario, the possibility, that at some point in the course of the referendum campaign next year or the year after that the No side moves to the front of that referendum.
“In order to try and get the result the Prime Minister would wish – that he wants a Yes result – he needs a last-minute initiative.
“And with no rules or restrictions saying new political initiatives should not be made at a government level in the last 28 days of the campaign, what would stop such a Prime Minister at that time doing a tour of European capitals, suspending question time in the national parliaments and flying here to London to announce a new commitment, a new undertaking, a new pledge – a new vow?
“To say only if you vote Yes, we will secure these new terms we didn’t mention before the campaign started.
“How would people in the United Kingdom then view that sort of situation?”