The council told the BBC the suspension would allow a full investigation to be carried out.
Concerns were raised about the contract last year by Birkenhead MP Frank Field who referred the matter to the Serious Fraud Office and District Auditor.
The focus was the Highway and Engineering Services Procurement Exercise (HESPE) contract which was set up in an attempt to bring several contracts together to cut costs.
The council previously had a number of small contracts covering areas like road maintenance and street lighting.
The HESPE deal brought all those elements under one large contract.
A statement from Wirral Council said: “In order that a full investigation can be conducted into matters raised by the District Auditor into concerns relating to the HESPE contract, the director of technical services will not be in the office whilst this further investigation takes place.
“It would be inappropriate to comment further at this time.”
Colas is the council’s current highways partner.