Rais told the official Bernama news agency: "In this case, although we don't have diplomatic relations with Israel or direct trade with the country, we don't have objections over their visit.
"They are a sports team with two Israeli members. We don't see it as something wrong.
"We have to look at this on a case-by-case basis. We don't want to mix politics with sports."
Chelsea are due to play the Malaysia national team in Kuala Lumpur on July 29.