The government has paused plans to carry out daily testing of students and staff in English secondary schools and colleges, following a warning that more research was needed to evaluate the benefits of the programme.

Public Health England and NHS Test and Trace said on Wednesday that the emergence of new, more transmissible variants of the virus meant that the pandemic had entered a “new phase” and as a result the balance between the risks of keeping children in school and benefits of daily contact testing within education settings was “unclear”.

A joint statement by the health bodies said: “In light of this changing situation, we now recommend that the rollout of daily contact testing within schools is paused, other than for schools involved in further evaluation.

“This will enable the further detailed evaluation of changing circumstances including, potentially, lower infection rates and modelling work required to understand the benefits of daily contact testing in this new phase of the pandemic.”

In December, the Department for Education announced that if a student or staff member was identified as a close contact of an individual who had tested positive, they would be eligible for daily coronavirus testing for seven days, instead of having to self isolate.

The intention behind the policy, which was to be rolled out in secondary schools and colleges throughout England following successful pilots in late 2020, was to maintain attendance within schools and was hailed as a “milestone moment” by education secretary Gavin Williamson.

Unions including the Association of School and College Leaders, which represents senior staff, said they supported testing for all children as a precautionary measure before they return to school, but have for several weeks warned the government against testing of Covid-19 patients’ contacts.

“This use of these tests never really made sense because they don’t detect all those with the infection, so we could potentially have ended up with more infectious people in school than under the self-isolation system where close contacts are sent home,” said Geoff Barton, ASCL general secretary.

“Unfortunately, the government’s insistence on first trying to use them in this way and then having to do yet another policy reversal will have thoroughly confused parents, pupils and the wider public. Schools will once again be left having to unpick the confusion caused by the government.”

The government U-turn follows growing concerns surrounding the reopening of schools within England. On Tuesday, Jenny Harries, England’s deputy chief medical officer, said it was “highly likely” that schools would reopen at different times across the country after the February half term.

“On the broad epidemiology it is highly likely that when we come out of this national lockdown we will not have consistent patterns of infection in our communities across the country,” she told the House of Commons education select committee. “And therefore as we had prior to the national lockdown it may well be possible we need to have some differential application.”

The government has said that it accepted the recommendations from PHE and NHS Test and Trace and said that while daily testing would be paused, there would be “no change to the main rollout of regular testing” throughout schools and colleges. The testing of teaching staff will also be increased to twice a week.

A government spokesperson added: “Daily contact testing, used as an alternative to up to a whole class having to isolate if a positive case is detected, continues to have the potential to be a valuable tool to keep more young people and staff at school, the best place for students’ development and wellbeing.”

“We will continue pilots to gather further data and to build the evidence base for the programme.”