The confusion reflected the chaos that has engulfed the country after a disputed parliamentary election triggered mass protests.
According to the office of President Sooronbai Jeenbekov, the state of emergency in Bishkek is to last from 8pm on Monday to 7am on October 19 and implies a curfew, a ban on rallies and other public events, and travel restrictions.
The new decree also reiterates the order to deploy troops to the capital to enforce the measure.
Mr Jeenbekov’s previous decree declaring a state of emergency in Bishkek was signed Friday, when a protest in the city turned violent and gunshots were fired at several political leaders.
It became void on Monday, as politicians did not consider it within three days.
Kyrgyzstan, a country of 6.5 million located on the border with China, plunged into chaos last week after mass protests erupted the day after a parliamentary election appeared to show parties connected to the ruling elite winning.
Protesters stormed and seized government buildings, looting some offices, and the central election commission responded by nullifying Sunday’s balloting.
Members of some opposition parties announced plans to oust Mr Jeenbekov and form a new government.
An emergency parliament session on October 6 named former parliamentarian Sadyr Zhaparov as a new prime minister, but the move was immediately contested by other opposition groups.
Politicians voted on Saturday to seal Mr Zhaparov’s appointment, but Mr Jeenbekov, who said he may consider stepping down only after the political situation in the country stabilises, is yet to sign a decree confirming it.
Protests in Bishkek continued most of last week, with supporters of rival factions occasionally clashing with each other.
Mr Jeenbekov declared a nearly two-week state of emergency in Bishkek on Friday and ordered the military to send troops to the capital in a bid to end the turmoil.
Convoys of military lorries were seen driving into the city, but it was not immediately clear whether police and the military would comply with the presidential order.
A curfew in Bishkek was announced on Saturday and amended Monday, following Mr Jeenbekov’s new decree, to last from 10pm to 5am.