Gove had said that the scale of demand from schools to escape town hall control required the government to rush legislation through parliament before this week's summer recess.
It now seems likely that no new academies will be formed in time for the autumn term as a result of the scheme.
The shadow education secretary, Ed Balls, accused Gove of "railroading" the legislation through parliament, and demanded that he explain why he "misleadingly claimed that more than 1,000 schools had applied". Balls, a contender for the Labour leadership, added: "It seems to me that the real reason for the rush was to avoid proper scrutiny for a deeply flawed piece of legislation."
Gove is already under attack from MPs, teachers and councils for a bungled announcement over whether hundreds of schools' plans for new buildings would go ahead.
He was forced to apologise in the Commons earlier this month after his office ignored advice to check an error-strewn list of cancelled building projects before it was published. The list suggested that many school building programmes would go ahead that had in fact been cancelled.
In relation to the academies, the department issued a press release on 2 June quoting Gove as saying: "The response has been overwhelming. In just one week, over 1,100 schools have applied." He added: "Of these, 626 are outstanding schools, including over 250 primary schools, nearly 300 secondary schools (over half of all the outstanding secondary schools in the country) and over 50 special schools."
Outstanding schools are to be fast-tracked to academy status.
A fortnight ago, the Department for Education revealed a second list of 1,907 primary, secondary and special schools that had registered an interest in turning into academies. Gove has written to every school inviting them to apply.
The new, far lower, number of schools that have applied may largely stem from the fact that Gove misdescribed expressions of general interest in the scheme as an actual application.
The lower-than-expected demand also questions why he needed to use emergency parliamentary procedures to rush through legislation this week. The academies bill, which became law on Tuesday, allows hundreds more schools to opt out of local authority control and turn into academies. The bill was pushed through the Commons in less than three days.
Balls said the emergency procedures were unnecessary given that only 153 schools had applied. He said Gove "railroaded" the bill through "because he said hundreds of schools wanted to become academies ... and many wanted to open [as such] in September. Now barely 10% of that number have even applied for academy status and none of them will convert in September."
It may be too early to say whether the level of demand to become academy schools is truly much lower than Gove had envisaged, but it would be a serious blow to the government's whole public service reform programme if it emerges that his revolution does not have the support in schools that he claimed.
Supporters of the scheme argue that school governing bodies are going to need time to weigh up the advantages of academy status, as well as see how some of the new schools perform. But the preliminary figures suggest that Gove's reforms have not sparked an instant nationwide revolution.
During the parliamentary passage of his legislation, Gove agreed to allow greater local consultation than planned before a school could take academy status.
The list of 153 schools includes about 45 primary schools, at least 12 faith schools and more than 20 grammar schools.
Gove has said he hopes – and expects – that academies will be the norm among secondary schools by the end of a first term in government. He told the Today programme earlier this month that "hundreds of schools are anxious to take advantage of these proposals".
Teachers' leaders condemned the government tonight for acting too hastily over academies.
"Our education system is too important to be subject to acting in haste, but repenting at leisure," said Mary Bousted, general secretary of the Association of Teachers and Lecturers.
"We remain concerned that many of the schools which have applied won't have carried out any form of consultation. Democracy will not be well served if children, parents and staff first learn of their school's plans to become an academy from the media."
She added that it would be "interesting to see if the list of schools applying to become an academy is as accurate, or not" as the error-ridden list that informed schools whether their building projects were to be scrapped.
Academies, unlike other state schools, have total freedom over their budgets, the curriculum and the length of the school day and term. They can also decide teachers' pay. Their expansion is thought to be the biggest change to school structures since grammar and secondary moderns were encouraged to become comprehensives in the 1960s.
Under Labour, only failing schools were turned into academies. But the new government has said that schools rated outstanding will be allowed to quickly switch to academy status and have their applications pre-approved.