The Kharkiv prosecutor's office said a probe was underway for a "terrorist attack" after a strong explosion in the city centre, which knocked out windows in a nearby university building and setting car alarms screeching.
The explosion damaged a flagpole with the national flag, but failed to knock it down, said a spokeswoman for the prosecutor's office.
The early morning blasts came weeks after the deaths of four people killed by a bomb that tore through a pro-government "Dignity March" marking the one-year overthrow of the former pro-Kremlin president, Viktor Yanukovych, on February 23.
The city of 1.4 million people is a major industrial centre with a large university population and is the capital of an area bordering the pro-Russian separatist regions of Donetsk and Lugansk, where a year of fighting between insurgents and the army has left more than 6,000 people dead.
It has been the scene of a string of bombings in the last months against military or strategic targets.
Kiev government officials say the attacks are orchestrated from Russia to destabilise a Russian-speaking region that harbours several aeronautical and aerospace firms as well as the Malyshev factories that manufacture tanks.
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