Before trading began, ministers and officials held a minute's silence to mark the country's earthquake and air disasters.
Finance minister Shunichi Suzuki then spoke.
He said the government had asked banks to make sure that people and businesses in the quake zone were able to access their money as normal.
Trading then got under way, and stocks were soon in the red.
The benchmark Nikkei index fell as much as 2% in early trade, before recovering some ground.
Analysts say the sell-off was sentiment-driven, following the country's tough start to the year.
By Thursday morning, 77 people were known to have died in the quake - Japan's deadliest since at least 2016.
Shares in construction firms bucked the down trend, rising sharply in early trades.
After an initial tumble, shares in Japan Airlines also rose.
The carrier lost one of its planes in a collision with a coastguard aircraft at Tokyo's Haneda airport.
All passengers were safely evacuated from the airliner, but five personnel on the coastguard plane were killed.
On Thursday, JAL said it would suffer a loss of around $105 million due to the incident.
Early probes suggest the airline's crew was not at fault.
Shares in the firm were up around 0.5% by late morning as investors weighed up the limited financial impact.
