The Birmingham education system feels almost as fragmented as the Balkans and some schools need a completely new ethos, Liam Byrne, a shadow minister and local MP has warned.

Ahead of a report that will find there has been an aggressive Islamist atmosphere in some schools, the senior Labour MP said the Birmingham education system needed improvements and must be allowed to move on after several investigations into whether there has been an attempt by Islamist extremists to infiltrate state-funded establishments.

A report due to be published on Tuesday is likely to find there are signs of extremism in some schools but no evidence of an orchestrated "Trojan horse" plot to take over schools, which was exposed in a letter now thought to be a hoax.

A draft of the report leaked to the Guardian last week referred to "co-ordinated, deliberate and sustained action to introduce an intolerant and aggressive Islamist ethos into some schools in the city".

The report was commissioned by the former education secretary Michael Gove and written by Peter Clarke, the former head of the Metropolitan police's counter-terrorism command.

Ahead of the official publication, Byrne called on Nicky Morgan, the education secretary, to concentrate on raising standards in those schools and winning back the trust of parents, rather than resorting to Gove's "divisive rhetoric".

"What we've got to do now in our city is we've now got to move on. And what that means is that we need both governors and government who are committed to fostering that sense of common good. Now that means school governors who don't promote an ethos in which other faiths and ideas are done down," he told BBC Radio 4's Today programme.

"It does also mean that we need ministers who drop the divisive rhetoric which Mr Gove has used in the past, like 'draining the swamp', or people on a 'conveyor-belt to terrorism'. At times in East Birmingham we've felt like we are just a football in Michael Gove's culture wars. That has been deeply damaging to parents' confidence, they have felt alienated from what should have been a thorough inquiry into what was going on with their kids' education.

"So I'm afraid the task for Nicky Morgan now as secretary of state is to bring people back together. And crucially, they've got to tell us how we're actually going to raise standards in Birmingham because our school system is so fragmented it feels at times likes the Balkans. And what we now need is someone who's going to take clear ownership of raising school standards."

Byrne said the problem could not be described as "brainwashing" but represented a threat to "unity in the community".

"What you've got [is] a handful of governors in a handful of schools … about 2% of schools in Birmingham, who are promoting a kind of ethos that is not, if you like, fostering a sense of the common good but is fostering a depth in what sets people apart rather than what they've got in common," he said.

"Our task as public servants in a city like Birmingham that is so diverse is to build a unity in the community, and where you've got a threat to that, you've got to take it out as fast as you can."