Gulf Air says it has been unable to resume flights to Iran because the Iranian civil aviation authority has been slow to approve flight schedules, the official Bahrain News Agency said on Tuesday.
The Bahraini national carrier is hopeful of resuming services to Iran by the beginning of next year, the agency said.
"Work is ongoing with the concerned authorities to resume flights as soon as possible," the news agency quoted Gulf Air as saying.
Relations between Bahrain and Iran have been strained by Bahraini accusations that Iran is behind the anti-government unrest, something Iran denies.
Gulf Air's passenger numbers have fallen since the start of an uprising last year led by the Sunni Muslim-ruled island kingdom's Shi'ite majority. Although the uprising was crushed, anti-government protests continue.
Lucrative air services to Iran and Iraq, both Shi'ite-led, were suspended at the height of the anti-government protests in 2011, but the airline said in August they would resume from September 20.
Bahrain's Shi'ites, who made up a majority of the protesters, complain they have long been marginalised in political and economic life, a claim the government rejects. Bahrain's Sunni rulers have rejected the protesters' main demand for an elected government.
On Monday, Bahrain summoned Iran's charge d'affaires to protest against what it called interference in its internal affairs after the Iranian consul in Manama met Bahrain's leading Shi'ite cleric, Ayatollah Shaikh Isa Qassim.
Bahrain, an ally of the United States and host to the US Navy's Fifth Fleet, reinstated its ambassador to Iran in August, more than a year after withdrawing him following Tehran's criticism of its crackdown on Shi'ite protesters.