Troops have surrounded Garissa University College and are engaging the attackers.
Witnesses spoke of the gunmen firing indiscriminately and there are fears the casualty toll could rise.
It is not clear who is behind the attack, but Somali al-Shabab militants have regularly targeted Kenya.
Garissa and other border areas have been regularly attacked.
Exchange of fire
Some five masked gunmen are said to have stormed the university. There are reports that hostages have been taken.
Kenyan police said the gunmen shot guards at the main gate at about 05:30 local time (02:30 GMT).
Nearby policemen then engaged in a fierce exchange of fire and the gunmen escaped into the university buildings.
Security forces were now trying to "flush them out", a police statement said. It urged people to stay away from the area.
Two guards were confirmed killed at the main university gate, with two policemen and a student among the injured. But eyewitnesses spoke of many casualties inside the building.
The gunmen reportedly ordered students to lie down on the floor, but at least 27 are known to have escaped and are at a military facility.
The BBC's Bashkas Jugsooda'ay in the town has spoken to one teacher who said students had come to her house early in the morning, running away from the gunfire.
"It was horrible, there was shooting everywhere," student Augustine Alanga told the BBC's Newsday programme.
He said it was pathetic that the university was only guarded by two police officers in such a volatile area.
Kenyan Red Cross spokeswoman Arnolda Shiundu said there were about 30 casualties, four of whom were critical. Most had gunshot wounds, she told BBC World News.
Three people - two soldiers and a civilian - had been airlifted to the capital, Nairobi, she said.
The university opened in 2011 and is the only place of higher education in the region. It has some 900 students, 700 of them from other parts of Kenya.
The BBC's Anne Soy in Nairobi says that because of its proximity to Somalia, Garissa is an easy target for al-Shabab militants and there have been several attacks in the past.
She says that the UK and Australia issued alerts this week warning of potential terror attacks in parts of the country, including Garissa.
Garissa, 150km (90 miles) from the border with Somalia, has a large population of Kenyan Somalis.
Al-Shabab has carried out a number of attacks in Kenya since 2011, when Kenyan troops were sent to Somalia to help fight the militant group there.
The deadliest attack targeted the Westgate shopping centre in Nairobi in September 2013, when 67 people were killed.
Al-Shabab is fighting to create an Islamic state in Somalia and is banned as a terrorist group by both the US and the UK.
Source: bbc
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