The losses incurred on the bid will put further pressure on Amey, and coincides with its failure to win a £766m public-private partnership contract for Nottingham and Milton Keynes councils.
The two setbacks complete a disastrous year for Amey, during which it was hit by delays to the Tube PPP deal and its PFI arm came under intense scrutiny after changes in accounting practices led to a drastic profit write-down.
In July, Amey and consortium partner Bechtel were forced to pull out of the £500m Leeds Supertram scheme after a row over bid costs. The firms wanted to be reimbursed before proceeding with their tenders but the council refused.
In Manchester, a preferred bidder is expected to be announced in August with construction work due to begin next December.
The shortlisted bidders will now have to prove they have the money
Manchester Metrolink insider
An insider at Manchester Metrolink said the tenders put forward by the two preferred bidders would now be examined in detail.
He said: "The two consortiums' bids will face scrutiny, and the bidders will have to prove they have the money and can meet all the costs involved."
The tramlink scheme got the go-ahead last week after Greater Manchester Passenger Transport Authority and the Association of Greater Manchester Authorities agreed a funding package with the government.
The network will more than double in size from 39 km to 95 km, and is expected to carry about 45 million passengers a year. The scheme is expected to cost £820m and there will be a private-sector contribution of £300m.