Birmingham academies Park View and Nansen Primary - rated inadequate by Ofsted - will have their funding agreements terminated.
Park View Educational Trust said it may be removed from running the schools.
Oldknow Academy and Golden Hillock School, also rated inadequate, were warned they could lose funding unless concerns were addressed.
A head teacher at one of the Trojan Horse schools said parents tried to undermine her authority and descended on the school during an Ofsted inspection.
The head teacher, who wished to remain anonymous, said she heard parents speaking to an inspector about her.
She said she came close to quitting her job on a number of occasions but everything "fell into place" when news of the Trojan Horse letter broke.
"From 2012 I felt alone," she said.
"I did not know it was happening to other heads. If I had known, I could have rationalised it but at the time I felt embarrassed.
"I started thinking 'maybe it is me, maybe I'm doing something wrong.'"
On Monday, the watchdog published 21 reports into schools allegedly targeted as part of a hardline Muslim takeover.
Five of those schools, including Park View and Oldknow, were rated inadequate.
'Islamic-themed assemblies'
Birmingham City Council said it would work with Saltley School, the only local authority school placed in special measures, and the Department for Education to install a temporary governing board.
In a letter to Park View chairman Tahir Alam, education minister Lord Nash said there were "deep concerns" about the way Park View School was run.
The letter said: "I have decided under clause 5.6 of the supplementary funding agreement for the academy to give written notice of the Secretary of State's intention to terminate that agreement."
Lord Nash criticised the trust for failing to promote "spiritual, moral, social and cultural development of pupils".
"I am deeply mindful of the need to eliminate discrimination, advance equality of opportunity and foster good relations," he said.
A similar letter about Nansen Primary School, also addressed to Tahir Alam, said it would have its funding arrangement terminated.
Both letters invited the trust to respond before 4 July.
A spokesman for Park View School said they would challenge the Ofsted report through the appropriate legal channels.
They said terminating the funding agreement would mean the trust could be removed from the running of the three schools.
"What happens to the schools after that would be the decision of the secretary of state, as they are already academy schools under the remit of [the] Department for Education," they said.
In a letter to Dr Achmad da Costa, chair of Oldknow Academy Trust, Lord Nash said it was not meeting the requirements set out in its funding agreement.
"Therefore the Secretary of State is minded to terminate the funding agreement unless all the breaches are addressed promptly, in full, and to his satisfaction," it said.
Lord Nash set out a list of actions the trust must take before 4 July.
These included ending "less favourable" treatment of non-Muslims, ceasing segregation of boys and girls, and drawing up a plan to ensure a more "broad and balanced" curriculum.
Oldknow Academy declined to comment on the letter from Lord Nash.
A letter to Tahir Alam regarding Golden Hillock's funding arrangement set out a similar list of demands to be completed within the same timescale.
Ofsted chief Sir Michael Wilshaw said "a culture of fear and intimidation has taken grip" in Birmingham schools, while a number of head teachers had reported an "organised campaign to target certain schools in order to impose a narrow, faith-based ideology".
'Own agendas'
The report into Park View School said the academy's work to keep students safe, including from extremism, was inadequate.
It said external speakers had not been vetted properly and the school had allowed a guest with known extremist views to speak to students as part of Islamic-themed assemblies.
Park View and Oldknow trusts did not comment on the future but one of Saltley School's senior teachers said it hoped to boost its Ofsted rating.
Darren Turner was brought in as associate head teacher on Thursday as part of a partnership scheme with other local schools.
He said there had been "upset" among staff and pupils at Saltley's inadequate rating.
"This is all about moving forward, what happens next," he said.
"Behind these walls they've got some excellent teachers and they want to get back to doing what they are good at: teaching.
"When this school gets back to 'good' again we want to go further and become outstanding."
Parents at the schools have criticised Ofsted's reports and accused inspectors of bias.
Health professional Arshad Malik told the BBC the findings were  "alien" to his child's experience at Park View.
"â€ŽInspectors came with loaded questions," he said.
"People are trying to use this school to push their own agendas."
He said parents would like to invite Education Secretary Michael Gove to the school for an open meeting about Ofsted's findings and to talk about what evidence was found to support them.
Two schools at the centre of the Trojan Horse inquiry are to lose their government funding.