The ministry also warned against going to other states in the area since the riots could spread and disruptions in Assam could cause disruptions elsewhere.
Israeli citizens currently in Assam are asked to act according to instructions by officials such as the police.
The new citizenship law lays out a path of Indian citizenship for six minority religious groups from neighbouring Bangladesh, Pakistan and Afghanistan, which protesters in Assam say would convert thousands of illegal immigrants into legal residents.
On Thursday, at least two people were killed in Assam state when police opened fire on mobs torching buildings and attacking railway stations in protest against the rules.Reuters contributed to this report.