China and Indonesia have already demanded explanations from Australia over reports that Canberra's missions were being used to monitor phone calls and collect data as part of American surveillance.
The dispute erupted in the region this week following a story in the Sydney Morning Herald, which reported a top-secret map leaked by fugitive intelligence analyst Edward Snowden that showed 90 US surveillance facilities at diplomatic missions worldwide -- including in Cambodia, China, Indonesia, Malaysia, Myanmar and Thailand.
Widespread reports of US National Security Agency spying based on leaks by Snowden, including that the agency was monitoring German Chancellor Angela Merkel's phone, have already sparked a major trans-Atlantic rift.
Malaysian Foreign Minister Anifah Aman said his country on Friday summoned the US and Australian mission heads to "hand over a protest note in response to the alleged spying activities carried out by the two embassies in Kuala Lumpur".
The US was represented by its deputy mission chief Lee McClenny, as the ambassador was out of town, the minister said in a statement, without giving details of what transpired.
Anifah on Friday also met his Australian counterpart Julie Bishop on the sidelines of a regional meeting in Perth, expressing "deep concern of such reports (of alleged Australian spying activities) which have caused considerable anger amongst the Malaysian public".
"He further stated that such activities are not done amongst close friends as it could severely damage existing relations," the statement said, adding both ministers would work together "to manage the situation and to avoid it from affecting the close bilateral relations".
US Secretary of State John Kerry this week admitted US spying has sometimes gone too far.
Indonesia has also summoned both its Australian and US ambassadors, while China has called for "a clarification" from both sides.
Indonesian Foreign Minister Marty Natalegawa described the reported spying activities as "just not cricket".
The reaction from other Southeast Asian nations mentioned in the Sydney Morning Herald report was more muted, however, with Thailand, Cambodia and Myanmar seeking to downplay the issue.
Washington has been seeking to improve ties in Asia in recent years to counter growing Chinese dominance.