One of the problem jobs relates to the design and construction of a floating submarine jetty as first reported by the Enquirer which was finished more than three years late.
The other covers the design and construction of living accommodation and infrastructure at Faslane Naval Base.
At the end of last year Morgan Sindall booked a loss of nearly £15m on four problem contracts, including the Faslane jobs for MoD.
Both MoD contracts were transferred as part of the acquisition of the design and project services division of Amec in 2007.
Morgan Sindall has been locked in a legal battle to reduce the amount it must pay of a £93.6m cost overrun on the submarine jetty at Faslane.
In a trading statement this morning it said: “The Group has now received a specific court judgement on one discrete issue in advance of a future arbitration hearing on one of these contracts, which is at variance with the legal basis underpinning the current carrying value of the corresponding receivable.
“The board has considered the implications of this court judgement on that contract, its relevance also to the other contract and reviewed its available options.”
The firm added that as a consequence, an exceptional charge of £35m will be recorded in the half year results to 30 June 2015.
This reflected the board’s best current assessment of the likely outcome on both contracts.
Morgan Sindall said it would also review its options to mitigate and maximise ultimate recovery levels.
On current trading, Morgan Sindall said its committed order book as at 31 March 2015 was £2.7bn, up 2% from the year- end.
The performance of the construction & infrastructure division has been held back by the performance of several contracts in London and the South which will be worked through to completion in the first half of this year.
Increased volumes in fitout, coupled with improved operational efficiency, were now driving strong growth in performance said the firm.