Israeli farms were in need of fresh recruits last October as many workers left when the Gaza conflict erupted.
The Malawi government says Israel has deported 12 Malawian workers who deserted the farms where they were employed.
In a statement, Information Minister Moses Kunkuyu said the workers had valid visas to work on specific farms but had “breached their contract” by going to work at a bakery.
The 12 Malawians were among more than 40 foreign workers who were arrested while working at a bakery in Tel Aviv last week.
Mr Kunkuyu said it was illegal under Israeli law for a foreign worker to change jobs without following the right procedures.
He cautioned all Malawian migrant workers in Israel “to desist from such behaviour as it puts this country into disrepute”.
“Such behaviour may also reduce employment opportunities of the individuals concerned,” he said.
Hundreds of Malawians travelled to Israel last year to fill a labour gap on Israel’s farms after thousands of workers left at the start of Israel-Gaza conflict in October.
It came as part of a labour export deal signed between the two countries in 2022.
Last week, some Malawians in Israel told the BBC that low salaries were the reason that some of them had left their jobs on the farms to look for other work in the country.
