A first flight carrying 221 youths left the southern African nation for Israel on Saturday and more would be sent soon, it said.
Israeli farms, a valuable part of the economy, have lost thousands of laborers since the October 7 Hamas attacks triggered the Gaza war.
Some were foreign workers who returned to their home countries and some were Palestinians from Gaza, who had their Israeli work permits revoked following the attacks.
Some foreign workers were among the 239 people that Israel says were taken hostage by Hamas on October 7.
Malawi's Secretary for Labor Wezi Kayira said Israel was one of several countries targeted by a government labour export program aimed at finding jobs for youth and generating desperately needed foreign exchange.
Kayira emphasised the government's commitment to the safety of the men, stating that they will work at certified locations classified as "fit and safe" environments.
The flight left barely two weeks after Israel granted Malawi, which is gripped by an economic crisis, a $60 million aid package.
The government has faced criticism from rights and governance activists over the way the deal was handled.
The Human Rights Defenders Coalition condemned the government's "secrecy" regarding the labor export agreement, calling on authorities to ensure the protection of the workers' rights in Israel.
Gift Trapence, the HRDC chairman, urged the government to disclose details of the labor agreements with Israel and other countries.
William Kambwandira of the Center for Social Accountability and Transparency also called for disclosure of the terms of the labor export arrangement.
Malawi opposition leader Kondwani Nankhumwa condemned the deal in parliament last week as "an evil transaction."
"No sane parent can send his or her child to a country that is at war."
Malawi has built close links to Israel over the years, while other African countries have taken a harder line on Palestinian rights.
Malawi agricultural school graduates have previously been sent to Israel.
Soon after coming to office in 2021, President Lazarus Chakwera announced that Malawi would open a full embassy to Israel in Jerusalem, becoming the first African nation in decades to do so in the contested city.