External Affairs Minister S Jaishankar, who is on a visit to Sri Lanka, announced the launch of "Operation Ajay" in a post on X on Wednesday night.
"Launching #OperationAjay to facilitate the return from Israel of our citizens who wish to return," he said.
"Special charter flights and other arrangements being put in place. Fully committed to the safety and well-being of our nationals abroad," he added.
The first batch of Indians is expected to be brought back from Israel in a special flight on Thursday.
Shortly after Jaishankar's announcement, the Indian embassy in Israel said it has e-mailed the first lot of registered Indian citizens for the special flight on Thursday.
"Messages to other registered people will follow for subsequent flights," it said on X.
According to estimates, around 18,000 Indians are currently residing in Israel.
The multi-pronged attacks against Israel by Hamas militants from Gaza since Saturday and the subsequent Israeli retaliation have left around 2,150 people dead.
The Israeli authorities said more than 1,200 people, including 155 soldiers, have been killed in Israel, while the Palestinian side put the death toll in Gaza at 950.
On Wednesday, Jaishankar discussed the "crisis" in West Asia with his counterpart from the United Arab Emirates (UAE), Sheikh Abdullah bin Zayed Al Nahyan.
"Spoke to Foreign Minister @ABZayed of UAE this evening. Discussed the ongoing crisis in West Asia. Agreed to stay in touch," the external affairs minister posted on X.
Earlier in the day, the Ministry of External Affairs (MEA) said it has set up a round-the-clock control room in Delhi and separate emergency helplines in Tel Aviv and Ramallah to monitor the situation in Israel and Palestine and provide information and assistance to the Indian citizens.
The phone numbers of the control room in Delhi are 1800118797 (toll-free), +91-11 23012113, +91-11-23014104, +91-11-23017905 and +919968291988, and the e-mail ID is situationroom@mea.gov.in.
"In view of the ongoing developments in Israel and Palestine, a 24-hour control room has been set up in the Ministry of External Affairs to monitor the situation and provide information and assistance," the MEA said.
Following the escalation in the situation, the Indian embassy in Israel issued an advisory, asking Indian citizens to exercise caution.
"In view of the current situation in Israel, all Indian nationals in Israel are requested to remain vigilant and observe safety protocols as advised by local authorities," it said.