Employees discovered the bullet holes on April 1.
"This is a warning for us," said Ermurat Bapi, the newspaper's founder, adding, "We often deal with corruption and sensitive cases within the government."
Bapi ruled out hooliganism, but said he does not believe anyone in the government was involved in the damage.
"We cannot say that this was an action organized by the state to frighten us because currently Kazakhstan is trying to promote an image of being for democratic reforms and is changing its laws and regulations accordingly," Bapi said. "We don't think those in power would be interested in doing something like this. However, shooting two bullets through an office window could be considered to be someone's warning to our journalists."
Bapi has been an editor in chief of independent newspapers in Kazakhstan for more than a decade and says he's been on the receiving end of numerous threats.
In 2003, Bapi was tried and convicted of falsification of documents and tax evasion. He received a suspended jail sentence but was barred from working as an "editor" or "journalist" until 2009, which explains why his official title at "Taszharghan" is "chief reader."
Police say they have no information on who could have fired the shots.
The news of the shots came the same day that independent Kazakh websites reported that independent journalist Bakhytzhan Mukushev had died after being in a coma for seven months. Mukushev was involved in an automobile accident, one of more than a half-dozen independent journalists in Kazakhstan to be killed or injured in auto accidents.
Merhat Sharipzhan, director of RFE/RL's Kazakh Service, contributed to this report.