Tsai's office announced in a statement that Lin tendered his resignation on Sunday, saying that he had "accomplished his periodic tasks", and it was approved by the president.
Speculation was rife that Lin would be replaced. The government's popularity has been hit by a series of controversial policies, ranging from holiday cuts to pension reforms, as well as by worsening relations with China.
Beijing has cut all official communication with Tsai's government since she took office in May last year. Her Democratic Progressive Party, which traditionally leans towards declaring formal independence from China, has refused officially to accept that Taiwan is part of one China.
In a TVBS poll released last month, Lin's support fell to a record low of 19 per cent, while 44 per cent said he should be replaced against 26 per cent who said he should stay.
"I am happy that somebody will take over the heavy burden and I'm grateful that somebody is willing to do that... I'll accept the criticisms that are reasonable," Lin told reporters when asked about his low public support.
His replacement will be announced on Tuesday. There has been widespread speculation that the popular mayor of the southern city of Tainan, William Lai, will take over.
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