The figure was almost half the 7.5 percent reported by National Institute of Statistics of Rwanda (NISR) for the same period in 2016.
Wholesale and retail trade contracted by 6 percent, while agriculture expanded by 6 percent, the NISR said in a statement.
Claver Gatete said he expected the third and fourth quarters to perform better than the first two, supported by stronger activity in construction, services and agriculture.
"There is a clear improvement and for the next two quarters we are going back to normal high growth," Gatete said.
A new GDP projection for 2017 will be issued around October after a meeting with a team from the International Monetary Fund, Gatete said. The current growth forecast for the year is 6.2 percent.
The central bank’s repo rate-setting body is due to meet on Wednesday.