The future of the city academies programme has been thrown into doubt by allegations over the abuse of honours, say teaching unions and MPs.
Mr Smith was the subject of a newspaper investigation (Photo: Sunday Times)
The warnings came after a head teacher who helped find wealthy sponsors for academies was arrested and later bailed as part of the cash for honours probe.
Des Smith, 60, quit the academies scheme after a paper accused him of promising honours to financial backers.
Police refuse to confirm reports they will also interview party lenders.
Mr Smith, who had already resigned from his post with the Specialist Schools and Academies Trust (SSAT), is expected to release a statement through lawyers after Easter.
Seven academy sponsors have been honoured since Labour came to power.
Teaching unions have said that the system of relying on wealthy businessmen to sponsor city academies must now be reviewed.
Under the government's scheme to turn round failing schools, the government adds about £25m for new buildings to each £2m private donation.
National Association of Head Teachers general secretary Mick Brookes said the whole programme was now in doubt.
"The notion of getting on board private finance is an attractive one, but this, I think, has thrown that notion into some question," he told BBC Radio 4's The World at One.
"I think we need a series of discussions as to whether this has a viable future."
Leader of the National Union of Teachers, Steve Sinnott, said that wealthy businessmen should not be able to exert significant influence over the way academies are run.
"We welcome good links between schools and business," he said.
"What we will continue to oppose is people being able to peddle in our education system their narrow beliefs and prejudices because they are prepared to put £2m into a school."
Labour MP David Chaytor MP, of the education select committee, told The World at One he feared the latest allegations raised questions about the scheme.
"What we have here with the SSAT is almost a Department for Education and Skills outside the Department for Education and Skills, and that raises all kinds of questions of accountability."
Set up in September 2005 the SSAT helps the government recruit education sponsors. Its president is Lord Levy, Tony Blair's chief political fundraiser and close friend.
Mr Chaytor added: "Certainly the model whereby it is one individual buying a significant amount of influence for £2m, I don't think is acceptable," he said.
He said Prime Minister Tony Blair's desire to push through education reforms as quickly as possible may have caused some of the current problems.
"I think that that sense of urgency has probably led to the cutting of some corners - for entirely the best of reasons - and I think we are seeing that in the issue that has been highlighted this week," he said.
But Education Minister Bill Rammell insisted that academies had been responsible for raising standards in some the the poorest parts of the country. He denied that sponsors were promised OBEs, knighthoods or peerages.
"Academies are a good thing and it is a good thing as well that individuals of their own free will and volition are actually contributing to this process," he told the World at One.
"Yes, they can be considered for an honour but there is certainly no guarantee and nothing we have done would suggest that that is the case."
There are also concerns potential donors will now be put off getting involved in controversial programmes such as the academies scheme.
Liberal Democrat MP Alan Beith, chair of the constitional affairs committee which will be looking into the cash for honours allegations, said both the party funding and academy sponsors issues raised questions about propriety.
He said genuine people with money to donate may think twice about funding controversial government programmes for fear of being caught up in a row.
The issues had developed "to the detriment of public philanthropy" he told Radio 4's PM programme.
The cash-for-honours inquiry was originally launched in response to a complaint by Scottish and Welsh nationalist MPs that Labour had broken the law preventing the sale of honours such as peerages and knighthoods.
Labour went on to reveal it had been secretly loaned nearly £14m ahead of the last election. The Conservatives were loaned a total of £16m by 13 wealthy backers.
The inquiry has since been widened to cover the activities of other parties.
Deputy Assistant Commissioner John Yates, who is leading the police investigation, has said he is prepared to consider more general allegations of corruption.