Police reportedly tear-gassed some rioting supporters after Arema FC lost 3-2 to rivals Persebaya Surabaya in East Java.
Around 180 were said to be hurt in a stampede with the disaster one of the world's worst at a stadium.
The country's chief security minister Mohammad Mahfud said 42,000 tickets had been told for the 38,000 capacity stadium and posted on Instagram: "To the victims family, our condolences. We also hope that the victims' families will be patient and continue to coordinate with the government officials in the field.
"I need to emphasize that the tragedy of Kanjuruhan is not a clash between Persebaya supporters and Arema. Because Persebaya supporters can't watch at that match. Supporters in the field are only from Arema.
"Therefore, the victims generally died from pushing, squeezing, trampling, and shortness of breath. There were no victims of beating or harassment between supporters.
"The government has made improvements to the implementation of football matches over time and will continue to improve."
Fans reportedly ran onto the pitch after the final whistle and police then fired tear gas, leading to the stampede.
The Indonesian football association (PSSI) has launched an investigation and Indonesia president Joko Widodo has ordered the league to be halted.
"I express my deepest condolences for the football tragedy that took lives in Kanjuruhan, Malang," he wrote on Twitter. "Due to this incident, I ordered the PSSI football league to be temporarily suspended until evaluation and security improvements were made."
Nico Afinta, police chief in East Java, said two officers were among the dead and added to a news conference: "It had gotten anarchic. They started attacking officers, they damaged cars.
"We would like to convey that not all of them were anarchic. Only about 3,000 who entered the pitch."