The debt office said 18.12 billion naira of three-month paper was sold at 5.99 percent, up from 5.74 percent at a sale on March 3.
It raised 13.68 billion naira of six-month debt at 8.30 percent against 7.95 percent, while a total of 83.17 billion naira of one-year paper was sold at 9.55 percent compared with 9.15 percent previously.
Total subscription fell to 323.47 billion naira from 409.84 billion naira at the previous auction.
The central bank on Tuesday raised its benchmark rate to 12 percent from 11 percent, having cut rates only four months ago by 2 percentage points, and lifted the cash reserve ratio for commercial banks to 22.5 percent from 20 percent.
Yields on fixed income paper rose after the central bank rate hike.
Three-month bills closed at 7.28 percent on the secondary market on Wednesday, up from 4.92 percent before th rate rise.
Six-month paper traded at 8.97 percent, up from 6.84 percent on Tuesday, while one-year paper closed at 10.01 percent against 7.77 percent previously.
Africa's biggest economy issues treasury bills to banks and non-financial institutions to help ease government cash flow, manage banking system liquidity and curb inflation.