Parliament unanimously passed the resolution after concluding that Kyrgyz law-enforcement agencies had not done anything to combat organized crime during Tashtemir Aitbayev's tenure.
This is the third resolution the Kyrgyz legislature has adopted trying to oust Aitbayev since last July. The president did not respond to the first two.
Aitbayev said Thursday's motion was politically motivated.
"Many deputies almost see me as their personal enemy," he said.
But Aitbayev said he would not resign.
"My post is determined exclusively by the president and I will follow his orders," he said.
Parliament's no-confidence vote came just a day after Prime Minister Felix Kulov had publicly accused Aitbayev of links with organized crime, saying the National Security Service chief was one of those responsible for the failure to combat crime and corruption.
Aitbayev responded by saying he held some incriminating evidence concerning the illegal sale of military aircraft and guns to Tajikistan and that Kulov, allegedly involved in the deals, had acted out of fear that the information would be disclosed.
