Sefton Central Labour MP Bill Esterson said he was disappointed that two borough schools have gone ahead with academy status.
Both Deyes High and Maghull High governors last week approved plans to make the move despite opposition from parents and campaign groups.
Pupils at Deyes High even staged a walkout after they found out about the decision.
While Deyes had balloted parents and staff over the decision - with the result coming back "overwhelmingly against" - Maghull High decided to leave the decision to just the governors which the Lib Dem chair of governors said had been "overwhelmingly" in favour.
Labour MP Bill Esterson said he was saddened the schools went against the views of parents and the wider community.
Bill said: "I am very disappointed that the decision was taken against the views of the parents and staff.
"Despite the assurances of the headteachers, there is a lot of fear that the schools, which are both outstanding schools already, will suffer because of this move.
"The headteacher at Maghull High has given assurances that there will be no staff cuts or redundancies. But as yet, he doesn't know what funding he will receive.
"My fear is that our children will be worse off because of the cuts in funding. Local authorities are suffering because of the cuts and the shift of funding from the local authority for academies will make that worse.
"These cuts are bad news for all schools, including those which become academies.
"I can understand that governors want to do the best for their schools, and they think that going for academy status will help them improve, but as the headteacher has said, there is no guarantee that there will be more cash made available."
Bill said he hoped that the Lib Dem chair of governors for Maghull High would use his influence to ensure the best for the school.
Bill said: "Molyneux Ward Lib Dem Councillor Geoff Howe has been spearheading Maghull High's decision to convert to academy status, despite the public demonstrations and concerns of parents and staff.
"I hope he can use his influence within his Tory-Lib Dem government to get the best for Maghull High. And I hope he can use his influence as a Lib Dem Sefton Councillor to ensure that he can get the best deal for all schools in the borough regardless of whether they go for academy status or not."
Labour Molyneux Ward Councillor Tony Carr, whose two sons attend Deyes, said he had been contacted by lots of other parents from both Maghull high schools, who were deeply concerned about the impact of going for academy status.
Cllr Carr said: "My two boys go to Deyes, I already know it is an outstanding school. I, and the parents and staff who have contacted me, don't want to see that jeopardised.
"I am concerned that the schools went ahead regardless of the views of the parents and staff. Their views were clear to see and hear from all of the demonstrations which were held and letters which were sent. They have some very valid concerns which have yet to be answered.
"I hope for the sake of our children that the governors have made the right decision."