According to President Petro Poroshenko’s website, the national flag was raised in Artemivsk and Druzhkivka.
It comes a day after government forces regained control of a key rebel stronghold at Sloviansk.
Meanwhile, a crowd of several thousand people attended a rally in the regional capital, Donetsk, in support of the rebels.
Rebel fighters have re-grouped in Donetsk and are reported to have attacked the state prison guard headquarters in an attempt to seize weapons.
However, Artemivsk and Druzhkivka are not considered as strategic as Sloviansk, but re-taking them indicates momentum is currently with government forces.
Despite their recent losses, the rebels still hold the regional capitals of Donetsk and Luhansk and other key areas.
However, senior Ukrainian security official Mykhaylo Koval said Luhansk and Donetsk would now be besieged until separatist forces there surrendered.
At the rally in central Donetsk, separatist fighters were cheered by thousands of supporters waving the flags of Russia and of the self-proclaimed Donetsk People’s Republic.
Many called on Russian President Vladimir Putin to come to their aid.
Correspondents said armed fighters from Sloviansk could be seen walking through Donetsk on Sunday, many still wearing military camouflage.
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