Schools minister Vernon Coaker made the move due to slow progress by ULT in turning around some of the "challenging" schools it took over.
Of the 17 academies it runs Ofsted inspectors recently judged two in Sheffield to be inadequate.
Coaker has allowed two academies ULT is planning to open, in Northampton and Oxford in September next year, to go ahead.
In a letter to both Oxfordshire and Northamptonshire county councils Coaker said: "It is quite clear that ULT has been bold and courageous in taking on some of the most challenging predecessor schools in the country. While there are encouraging signs, equally, there is still some way to go before all ULT academies are making the consistent progress.
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