"The market had expected this change right after the government released data on the trade deficit," a money market dealer at a Vietnamese bank in Ho Chi Minh City said.
The previous depreciation was on Jan. 7, when the central bank also weakened the dong by 1 percent to help stabilise the foreign exchange market.
The State Bank of Vietnam said in a statement that recent pressure on the dollar/dong rate was "psychological" and "in market expectations", saying its latest move was to help meet socio-economic targets and cope with negative impacts from global markets.
"The (market) expectation is more depreciation as the dong is down just 2 percent while other currencies in the region have fallen 4-5 percent now," he said.
Read MoreWhy Vietnam's positives aren't boosting stocks
Last December, central bank Governor Nguyen Van Binh said it would keep the dong depreciation to less than 2 percent for the whole of 2015.
After Thursday's adjustment, the dong fell to 21,650/21,730 per dollar on the interbank market, from 21,620/21,670 the previous day.
Vietnam's January-April exports rose 8.2 percent to an estimated $50.1 billion, while imports surged 19.9 percent.
The government has projected annual export growth of 10 percent for the whole of 2015, slowing from a rise of 13.7 percent last year.