The MoU, along with another pact on security cooperation, was signed before the talks between Prime Minister Narendra Modi and German Chancellor Angela Merkel and exchanged during media interaction of the two leaders.
The MoU on "carriage of in-flight security officers within a short time fame" was signed by Minister of State for Home Affairs Kiren Rijiju and his German counterpart Gunter Krings.
Rijiju and Krings discussed the threat posed by ISIS terrorist group and ways to cooperate to counter it.
"Such extremists elements based in Germany often utilise their places of religious worship to support extremist organisations in India by propaganda and financing. The flag of Khalistan and photographs of terrorists bearing weapons are openly displayed in many Sikh religious places in Germany to incite hatred and anger," the Indian Minister told Krings.
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The annual report of the Protection of Constitution published in June 2015 has made specific reference to 'Extremist Sikhs' in the list of extremist organisations of foreigners in Germany.
Rijiju said Germany is an important power house and trade partner and signing of the pact will ensure that extremist forces are kept in bay.
"My counterpart was very positive to the issues raised by us and assured full cooperation to India in this regard," he told reporters.