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A former Department of Agriculture and Food manager has been charged with two counts of corruption after he allegedly stole more than $5000 from the department to pay for works done on his house.

The 53-year-old North Perth man, who was responsible for capital works and building maintenance at the department, was charged after he was investigated by the Corruption and Crime Commission.

The CCC says the man had work done on his house by a friend who owned a building maintenance contracting business in 2009.

After he realised he could not pay for the work, he allegedly organised for the contractor to do two fake maintenance jobs for the department worth $5500.

It is alleged the department paid the contractor for the work, which was never done.

The man is due to appear in the Perth Magistrate's Court on February 11.