Eight academy schools have been put on notice that they must boost their standards or face action, it was revealed today.
Education Secretary Michael Gove said the schools have been issued with pre-warning notices because they are severely under-performing.
It comes as MPs raised concerns that a government quango responsible for investigating complaints against academies is failing to do so.
Taking evidence from Mr Gove during a session of the Commons education select committee this morning, chairman Graham Stuart suggested there was confusion over whether it was in the remit the Young People's Learning Agency (YPLA), which had its responsibilities transferred to the Education Funding Agency (EFA) this month, to investigate such complaints.
Ministers had previously said that parents or local authorities who had a complaint about an academy could take it to the YPLA, he said.
"And yet, we are told by the Special Education Consortium (SEC), among others, that their members frequently reported that when parents called the YPLA, they were advised that handling complaints against academies was not within their remit.
"How can both of these things be the case?"
Mr Gove told the cross-party group of MPs he believed that the YPLA, now the EFA, had been "effective" in dealing with problems with academies, and knew of cases where action has been taken.
He added: "There are eight academies where the level of under-performance has been such that my department has issued pre-warning letters. Warning notices may follow as a result of that and action will be taken.
"I can only apologise to any individual who feels that the recourse to making complaints has been inadequate so far, and I'll look into the specific concerns that have been raised."
Mr Stuart said that enquiries by the SEC suggested that the EFA appears to be unaware that it should be investigating complaints about academies.
"That's a fairly extraordinary situation for an organisation as well organised and thoughtful as the SEC," he said.
Mr Gove said that sometimes there can be "mutual misunderstanding".
But he added: "It manifestly cannot be the case that the YPLA or EFA is unaware of its responsibility to investigate, when it has been investigating one particular academy, one particular educational institution, where there are causes for concern."
Asked by Mr Stuart if he was confident that the complaints system was working properly, Mr Gove said that up to this point he had been confident that they were being dealt with effectively.
"You have drawn to my attention a specific concern raised by a reputable body and of course it is my duty to look into that," he added.
Academies are semi-independent state schools, that receive their funding directly and have freedom over areas such as staff pay and conditions and the curriculum.
The first academies were set up under Tony Blair's Labour government with the aim of turning round failing schools in disadvantaged areas. They are known as sponsored academies.
As well as continuing to open sponsored academies, the coalition Government has opened up the scheme to allow all schools to apply for academy status. These schools, which have usually been rated good or outstanding, are known as converter academies.
The Department for Education today said it was not naming the eight academies that have been issued with pre-warning letters, but it is thought they are more likely to be sponsored academies than converters.