Some 470 Taiwanese stranded in the Chinese province of Hubei were due to return to the island on Tuesday night following a compromise between Beijing and Taipei.
The repatriation comes more than a month after the first batch of 247 who had been stuck in Wuhan, the centre of the Covid-19 outbreak, health minister Chen Shih-chung announced earlier in the day.
Talks about repatriating the 1,000 or so Taiwanese remaining in Hubei had foundered as the two sides started "playing politics", as one observer described it, over sovereignty.
Taiwan also complained that an infected person had been returned to the island, undermining its efforts to contain the disease.
"The two sides have agreed on the method and the list of the people who are to be sent back," Chen said.
The 470 were due to return on Tuesday night on two separate planes dispatched by Taiwan's China Airlines and the mainland's China Eastern Airlines.
Both flights would have a 13-member medical team to help in the plane for quarantine and other health care, according to Chen.
"All those passengers need to be tested before they are allowed to board the planes," he said, adding upon arrival, those passengers will receive yet another round of medical checks before they are sent to the island's quarantine centres for two weeks.
Around 600 Taiwanese will still be stranded in Hubei after the second round of repatriations, according to Taiwan's semi-official Straits Exchange Foundation, which deals with the mainland.
When asked whether the 600 would be returning to Taiwan soon, Chen replied: "We will see what to do after the (repatriation) this time" - a suggestion that Taipei would wait to see whether this evacuation was in line with its expectations before resuming talks.
Taiwan asked to arrange for evacuation soon after Wuhan was locked down on January 23, but the two sides fell out after the mainland dispatched a China Eastern Airline plane to carry 247 Taiwanese back, one of whom was found to have contracted the coronavirus that causes Covid-19.
Following the discovery, the Taiwanese side rejected a proposal from the mainland authorities that they would dispatch more China Eastern Airlines flights to send the remaining Taiwanese back.
"Obviously the two sides are playing politics over the issue as both wanted to exercise their sovereignty over the repatriation," said political commentator Jaw Shaw-kong.
Beijing, which sees Taiwan as a breakaway province that must be returned to the mainland fold by force if necessary, does not want to create the impression that the Taiwanese are being evacuated like foreign nationals.
By contrast, Taipei hopes to play up the evacuation flights to highlight its sovereignty, Jaw noted.
Former president Ma Ying-jeou has called for the two sides to take a step back to allow charter flights from China Airlines and China Eastern Airlines to carry the stranded Taiwanese back out of humanitarian concern.
Taiwan's mainland-friendly opposition Kuomintang, which has been highly critical of what it regards as the government's stalling of the evacuation due to political concerns, said the compromise between the two sides over the repatriation issue signals a "good start".
"But there are still some 600 of our compatriots stranded in Wuhan, including those who need to return to Taiwan for schooling," the party said in a statement calling on the two sides to continue to negotiate in goodwill to allow the remainders of the Taiwanese to return home as soon as possible.
But the Mainland Affairs Council, the island's top cross-strait policy planner, said detailed negotiations between authorised channels were needed while full preparatory measures were needed to prevent the outbreak from intensifying on Taiwan.
On Monday, Premier Su Tseng-chang stressed the evacuation of the stranded Taiwanese by charter flights must be in line with the principle of prioritising minority groups and those who have chronic diseases. He said the evacuation must not compromise the government's efforts in containing the outbreak.
Taiwan has now recorded 47 cases of coronavirus infection, including one death.
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