The results compared with a deficit of $21.6 billion in the same period a year earlier.
The Finance Department said the results were in line with the March budget which projected a $25.9-billion deficit after the year-end adjustments.
Federal government revenue for the 12-month period totalled $253.9 billion, up by $3.4 billion from a year earlier, helped by higher income tax revenues, tariffs and Employment Insurance premiums.
Program spending totalled $243.2 billion, up by $2.7 billion due to an increase in the amount of money transferred to the provinces and to individuals.
This was partially offset by lower program expenses.
Public debt charges were $29 billion, down by $2 billion.
Sonya Gulati, a senior economist at TD Economics, said the "whopping" $6.5 billion deficit for March brought the fiscal monitor numbers in line with the government's projected deficit.
"All along, Fiscal Monitor numbers seemed out of sync with official deficit estimates in fiscal update and budget documents," Gulati said in a note.
"We were waiting for either significant improvement in the deficit tally come Public Accounts time or a sizable deficit in March. We got the latter."