The current rules on social gatherings and venues were imposed in mid-May when domestically transmitted cases surged.
Central Epidemic Command Centre (CECC) Chief Chen Shih-chung told a news conference that the alert would now last through July 12.
New cluster infections were found in certain traditional markets, nursing homes and construction sites in northern Taiwan, where capital Taipei sits.
“The situation has been nevertheless improving,’’ Chen said, urging residents to remain cooperative.
Virus control measures were further tightened in all agricultural wholesale markets in northern Taiwan.
On Wednesday, the CECC announced 104 new locally transmitted coronavirus cases and 24 related deaths.
Since the pandemic began, Taiwan has confirmed a total of 14,260 coronavirus infections.
As at Wednesday, the death toll had reached 599.