The commission annulled the results in the regions of Sumgait and Binaqadi. It also annulled the results in 10 out of the 28 polling stations in Surakhani, where leading opposition figure Ali Kerimli ran.
The ruling Yeni Azerbaycan (New Azerbaijan) party won by far the most seats in parliament, according to partial official results.
The opposition has rejected the election results, citing massive irregularities and called for a repeat vote. Monitors from the Organization for Security and Cooperation in Europe and the Council of Europe said the vote failed short of international standards.
The EU Presidency today urged Azerbaijani authorities to fully investigate the alleged irregularities.
President Ilham Aliyev, in televised comments yesterday, played down the criticism but acknowledged irregularities in a small number of districts. He promised to punish the officials responsible.
"The goal of the Azerbaijani government and of the Azerbaijani president has been to hold free and fair elections," Aliyev said. "That is why I cannot allow any official to cast doubt on the overall results of the elections by his arbitrary actions or illegal interference."
Russian Foreign Ministry spokesman Mikhail Kamynin described the OSCE monitors' assessment as "hasty."
(RFE/RL's Azerbaijan Service/AP/AFP/Interfax/ITAR-TASS)