A high level review of the way expert witnesses are used in child abuse cases in family courts is to take place.
Expert evidence was discredited in the case of Angela Cannings
Children's Minister Margaret Hodge said Chief Medical Officer Sir Liam Donaldson would carry out the inquiry.
It follows the case of Angela Cannings, cleared of killing two of her children when expert evidence was ruled unsound.
Mrs Hodge also released the results of a first review into disputed cases of children being taken into care, which has questioned 47 out of 5,175 cases.
She said the government's moves were in response to "widespread concern" about the "quality and validity of evidence" given by medical expert witnesses in court.
The review asked local authorities to look at how many cases where children are currently in the process of being taken into care could be affected by the Cannings judgement last December.
A spokesman for the Children's Minister told BBC News Online nine of the 47 cases questioned had been concluded, with a change of decision in only one.
In a statement, Mrs Hodge said: "The results of this survey should not give rise to complacency that the interests of children and their families are being optimally served."
She told the BBC Sir Liam's review would help ensure sufficient expert witnesses were available to courts.
"They play an important role in child proceedings and if we want to safeguard children properly, we need to have the best calibre medical witnesses working with the courts," she said.
Felicity Collier, chief executive of the British Association for Adoption and Fostering, said they were "very concerned" by difficulties in finding expert witnesses.
"We must find doctors who are able to give this evidence and who are prepared to do so," she said.
A couple who believe their children have been wrongly taken away by social services told the BBC the court had ruled against them on the basis of one medical expert.
"There was no conflicting medical evidence," the father said. "It was him and him alone and that power surely cannot be allowed to continue.
"He held the power completely over our whole family and with that power in one fell swoop he destroyed it."
Alan Levy QC, an expert in child law, said without a central accreditation system for medical witnesses, there was a danger experts who were "really not well qualified" could "slip through the net".
He said Mrs Hodge was "incredibly complacent" to let social services carry out an ongoing review of 30,000 past cases where children were taken into care on the basis of disputed medical evidence.
"To suggest the final person who should decide whether they should be looked into is the very party that brought the proceedings is completely unsatisfactory and will leave a bad taste," he said.
Shadow children's minister Tim Loughton also criticised the decision to let local authorities review their own past cases.
He said: "This will not inspire confidence that justice has now been done for every potential case of a child removed from parents unreasonably on questionable evidence."
The local authorities' findings are due in a few months' time and Sir Liam's report to ministers early next year.
The Court of Appeal decided to overturn Mrs Cannings' 2002 conviction for smothering her two sons after evidence from cot death expert Sir Roy Meadow was discredited.