According to the law, institutions teaching children under the age of 16 must be registered.
The Department for Education has a list of 23 Orthodox institutions in Stamford Hill, north London, which it believes are unregistered yeshivot.
Sir Michael said that the "full force of the law" should be brought against institutions operating outside the law. "Local authority officers acknowledge the problem, but too often use the excuse of bureaucracy, legislation or lack of resources as a reason for inaction," he wrote.
In response to Sir Michael's letter, Ms Morgan said that "since 2010 we have taken robust steps to tackle unregistered schools and improve safeguarding. However we agree with Sir Michael that more needs to be done."