The move comes amid Western criticism towards China over escalating military pressure on democratically ruled Taiwan, which China claims as its own territory, and Beijing's strengthening of ties with Russia during the invasion of Ukraine.
Relations between Lithuania and China worsened after the former allowed Taiwan to open a de facto embassy late last year.
Latvia's Foreign Ministry said the country's continued participation in the China group was "no longer in line with our strategic objectives in the current international environment."
In statements published Thursday, both Latvia and Estonia said they would continue to work towards "constructive and pragmatic relations with China" while respecting the rules-based international order and human rights.
Estonia's Foreign Ministry was not immediately available for further comment.
The Chinese embassies in Riga, Latvia and Tallinn, Estonia did not immediately respond to requests for comment.
Bulgaria, Croatia, the Czech Republic, Greece, Hungary, Poland, Romania, Slovakia and Slovenia are among countries that remain in the cooperation format.
The Czech Republic's foreign ministry said in May the promise of large Chinese investments and mutually beneficial trade were not being fulfilled, following calls within the country's parliament to quit the group.
(Reporting by Augustas Stankevicius and Terje Solsvik; Additional reporting by Michael Martina and Simon Lewis in Washington; Writing by Joanna Plucinska; Editing by Josie Kao and John Stonestreet)
By Augustas Stankevicius