Results from the Key Stage Two and Three Standard Assessment Tests for 11 and 14 year-olds were due to be returned to schools in three days' time but Schools Secretary Ed Balls announced yesterday that some papers would not be returned until after the start of the summer holidays.

The National Assessment Agency, which operates the tests, has apologised to schools, pupils and parents for the delay, blaming it on a "serious failure" by the private firm ETS Europe, which is in its first year of a five-year contract to carry out marking.

Mr Balls branded the late delivery of 1.2m test papers "completely unacceptable" and promised an independent inquiry would be launched. But the Normanton MP said he had been assured there were no problems with the accuracy of marking.

Most of the Key Stage Two Sats in English, maths and science taken in May by 11-year-olds are now due to be returned by July 15. The bulk of Key Stage Three marks for 14-year-olds in those subjects are expected at the end of that week – but it is thought likely that some will not be known until after schools have broken up for the summer.

Reports of difficulties have circulated for months. Teachers said they were unable to enter pupils' details on an online database, while markers complained of inadequate training.

ETS has employed two extra marking panels, based in Leeds and Cheadle, near Manchester. They will work seven days a week to clear the backlog.