The council has conducted an audit of work by the consultant since 2004.
Auditors claimed general inspections were not delivered according to contract.
Mouchel denied the allegation and said it had met the terms of the “service level agreement” which has now been renegotiated by Milton Keynes Council.
Auditors said they found evidence parts of a maintenance agreement for Milton Keynes’ 1,200 bridges were not being “adequately performed and other parts are disputed by Mouchel”.
A BBC Inside Out investigation found the council hired an external specialist who made 12 inspections and discovered repairs that would cost a minimum of £650,000.
Mouchel told the programme it had kept to the terms of its contract.
The report also criticised Milton Keynes Council for not overseeing the necessary work properly.
Council leader Andrew Geary said a lot of the work had now been brought in-house and a new subsidiary owned by the council hopes to complete it by the end of next year.
Geary told the BBC: “We are getting our bridge inspections up to date and we have done a huge programme of putting things correct.
“Mouchel won’t be carrying out many functions or services for Milton Keynes as of the end of December.”
“We believe bringing this work back in house… is the best value for the taxpayers.
“Yes, we had a fee that we paid them (Mouchel) every year to deliver services for us.
“It was a 12-year deal and we have paid to come out of that three years early.”
In a statement, a spokesman for Mouchel said it had “fully met the requirements” of the agreement it has had with the council since 2004.
“In the past year, Mouchel has completed a significant number of additional general bridge inspections over and above the contractual requirement,” the spokesman said.
The company said it had been asked earlier this year to provide extra services, including a three-year programme of bridge inspections that started in August.
The existing contract with the council, which has been extended by three years to 2018, has recently been “restructured” to provide “greater flexibility” to the council, the spokesman added.
