Merkel was on her way to India for an official visit. She arrived late in New Delhi on Tuesday morning as a result of the delay. The plane had a large delegation on board.
The government aircraft was denied overflight rights in the early hours of Tuesday. The exact reason for the denial of overflight rights is unclear. But before the plane left Berlin on Monday evening, it was reportedly given permission by Iranian authorities.
Germany along with the US and its other allies in NATO has long been at loggerheads with Iran essentially over its nuclear arms policy and alleged support to terror.
ANGELA MERKEL ON INDIA VISIT
On a one-day visit to India, German Chancellor Angela Merkel met Prime Minister Manmohan Singh in New Delhi today. The two held crucial talks and signed four agreements for cooperation in vocational education, medical research and science and technology. (Watch: PM, Angela Merkel hold talks, sign agreements)
"We are happy with Indo-German science and technology agreement today. We discussed south Asia and west Asia and reiterated the importance of a strong, prosperous and open Euro-zone. We look forward to strengthening Indo-German strategic partnership," Prime Minister Manmohan Singh said in a joint press conference after meeting with Merkel.
Merkel also said she was pleased with India-Germany consultations.
"India and Germany have strong international co-operation. Our 60 years of diplomatic ties have very good future. India is our partner on the road ahead," she said.
Merkel has also pledged German support to help India develop sources of renewable energy.
These talks are the first inter-governmental consultations between India and Germany at the cabinet level.
India is the first Asian country and one of very few nations with which Germany holds a joint cabinet meeting. This is seen as a demonstration of its high esteem for India as a long-standing and reliable partner and as recognition of India's rapidly growing economic clout and technological prowess.
In the evening, Merkel will attend a concert marking the opening of the "Year of Germany in India."
The Indo-German inter-governmental consultations were chaired jointly by Chancellor Merkel and Dr Singh and were attended by five German cabinet ministers as well as senior officials from several ministries.
GERMANY ANNOUNCES END TO NUCLEAR POWER BY 2022
In a landmark decision, Germany yesterday decided to phase out nuclear power by 2022. Germany's Environment Minister said that Chancellor Angela Merkel's coalition government has agreed to shut down all of the country's nuclear power plants by 2022.
Norbert Roettgen also said the seven oldest reactors taken off the grid pending safety inspections following Japan's Fukushima nuclear disaster in March will remain offline permanently.
He said all but the three newest reactors will be shut down by 2021, and the remainder a year later.
Roettgen announced the agreement early on Monday morning after hour-long negotiations between the governing parties.
Merkel in 2010 had pushed through to extend the lifespan of the country's 17 reactors with the last one scheduled to go offline in 2036, but she completely reversed her policy in the wake of Japan's nuclear disaster. She described the new move as a step that will make her country a pioneer in renewable energy.