Bowcott's appointment will give a boost to the engineering and construction group, which issued a profit warning at the end of last year. The firm's construction order book has fallen from £2bn to £1.8bn.
It is understood that Bowcott will oversee utilities and major project work in the UK. He will report to David Robson, Amec's chief operating officer in the UK.
Bowcott is to leave Mowlem next month and join Amec in the spring. Mowlem sources said his departure was amicable, despite the firm's terse statement announcing that that he was leaving.
One source said: "He accepted the job two or three months ago. He is very sorry to be leaving Mowlem."
Bowcott took over as building managing director from Brian May, now UK chief executive at HBG, in March 2000. Before that he was Mowlem's performance director and managing director of the southern division.
Bowcott will oversee Amec’s utilities and major projects in the UK
His departure came as Mowlem announced the merger of its building and infrastructure divisions, creating a construction services arm with a turnover of about £1bn.
The division will be headed by infrastructure boss Willie Smith and will start operating this month. Mowlem has also appointed Mark Keogh as finance director at the division – Keogh joins from BP Marine.
John Gains, Mowlem's chief executive, described the move as a logical step. He said: "I see it as a very positive step forward in developing the integrated construction solutions being demanded by our customers."
A source at the firm said the firm had been considering the restructuring for about a year.
He said: "It creates a good balance in the business, with a services and a construction division."