The yield on the 15-year bond rose to 12.388 percent from 10.923 percent at its last sale in December, while that of a new two-year bond also on sale came in at 7.439 percent from 5.284 percent at its last sale in February.
"The rise in rates is as a result of tightening monetary policy which as expected has reduced liquidity in the market in addition to the final payments of 2010 tax liabilities that has further reduced liquidity," central bank said in a statement.
The bank had offered a total of up to 18 billion shillings ($214.3 million) from the two bonds.
It received bids worth a total 10.4 billion shillings for the bonds, and accepted bids worth 6.23 billion shillings for them.
The bank said it would sell bonds worth a total of 16 billion shillings in May.
Last month the central bank raised its key interest rate for the first time since June 2008, increasing it by 25 basis points to 6.0 percent.
Fixed income traders had said they expected bond rates to go up after the key interest rate hike, as well as due to rising inflation rates.