Is what the purchasing agent does—giving suppliers unreal prices for the benefit of the company he works for—considered a lie, and will he accrue sins for it?

What you are doing is forbidden lying. It is obligatory for a Muslim to be truthful and trustworthy. It is not permissible to betray a trust or cheat by informing companies of an untrue price. Therefore, repent to Allah Almighty and be wary of His punishment.