Malaysia has been on high alert since an attack last January by ISIS-linked militants in the Indonesian capital Jakarta.
Inspector-General of Police (IGP) Khalid Abu Bakar said the suspects were detained in three separate raids from Jan 27 to Jan 29, Reuters reported.
It is unclear if all three are connected.
Mr Khalid said a 37-year-old Indonesian was arrested on Jan 27 in Kuantan, The Star reported
"He was working as a security guard at Malaysia Airlines. He had connections to Malaysian ISIS militants fighting in Syria as we also detected that he went to Turkey in 2013," he said in a statement yesterday.
The counter-terrorism division also seized an airsoft gun, added Mr Khalid.
"We discovered that the suspect planned to take his wife with him to Syria to join the ISIS there," he said.
Mr Khalid said the second suspect - a 32-year-old Malaysian was a security guard at a private company and he was also detained in Kuantan on Jan 27.
"We seized a shotgun from the suspect. The suspect also had plans to go to Syria," he said.
He said the last suspect - a 38-year-old Malaysian - was detained in Kuala Lumpur on Jan 29.
Said Mr Khalid: "He had threatened to attack the Negri Sembilan Mufti's department, claiming that it did not follow the teachings of Islam.
"He also threatened to bomb several locations in Kuala Lumpur." Malaysia has not seen a serious militant attack but authorities say they have disrupted several plots.