Is it considered a sin to work on projects that are referred by government employees in exchange for a percentage of the fee, knowing that this referral might be a result of exploiting their position?

There is no objection to performing the aforementioned transactions, whether they come directly from the customer or through a government employee. The sin of an employee exploiting his position and taking a bribe for work that he is obligated to do falls solely on the employee, and you have no connection to it. However, if the employee's interaction with the customer is outside the scope of his job and working hours, then there is no harm in him taking payment for that. One should have a good opinion of people and not accuse anyone without proof.