The new 472km (293 mile) railway cost close to three times the international standard and four times the original estimate.
A local newspaper reported on Monday that Chinese lenders could take control of the port of Mombasa if Kenya defaults on the $3.2bn (£2.3bn) loan.
But in a statement, the finance minister said "there is absolutely no risk of China or any other country taking over the port".
He said the loans for the railway cannot "be paid through any other fund or any other entity without the approval of parliament".
