Nato has sought to bolster its presence in the Middle East, and the accord is the first one to be finalised since the 26-member alliance offered in 2004 to forge closer ties with Israel and six Arab states, it said on Monday.
"Israel is the first one to have agreed to the details of what co-operation should entail," said a Nato official, adding that details of the pact would be released later.
The details agreed on Monday included a pledge to provide support for counter-terrorism patrols by alliance ships.
Nato has offered Israel, Algeria, Egypt, Mauritania, Jordan, Morocco and Tunisia help in reforming their armies and making it easier for them to cooperate with the military of alliance nations.
Algeria and Morocco have also expressed an interest in supporting the patrols, but the Arab response to offers of co-operation has been muted.
Many in the Arab world regard Nato as a US-dominated body that intends on interfering in Middle Eastern affairs.
Nato nonetheless held its first meeting in an Arab country this year with the seven Mediterranean partners in Morocco, and is looking to provide training for the countries, which include four Gulf states.
Diplomats say Jordan had shown interest in hosting a Nato-run academy but no final decision has yet been taken.