"We had intelligence inputs of ULFA targeting the city's crowded areas, a day ahead of celebrations to mark the state government's first year in power," a police official told the Reuters news agency.
Separately, police found an unclaimed steel box on Saturday on a train travelling from New Delhi to Gauhati during a routine check at a station stop 200km outside of Gauhati, T Rabha, a railway official, said.
Inside the box, police found a 10kg bomb, which the army later defused, he said.
Officials believe the incidents might be pegged to the state government's one-year anniversary of holding power, which is to be marked on Sunday with public events.
The state government is ruled by the Congress party, which also leads the governing coalition in New Delhi.
The ULFA, one of several separatist groups that have been fighting since 1979 for an independent homeland in Assam, has set off more than 20 bombs over the past two months, police said.
Peace talks between the ULFA and the Indian government broke down in September last year after a six-week truce. In January, at least 80 people were killed in a series of attacks blamed on the separatists.
The separatists say Assam's indigenous people, most of whom are ethnically closer to Myanmar and China than to the rest of India, are ignored by the federal government in New Delhi, 1,600km to the west.
They also accuse the government of exploiting the northeast's rich natural resources, which include oil, natural gas and tea.
New Delhi has launched a huge military offensive against the group and the Indian army says it has killed 55 separatists and arrested 553 others since January.
More than 20,000 people have been killed since the group began it's campaign began in 1979.