Janesville and Milton school officials canceled classes on Friday because Jakubowski is still on the loose.
The University of Wisconsin-Rock County and Blackhawk Technical College are also closed.
Subject of Janesville manhunt, Joseph Jakubowski, has sent a 160-page manifesto to President Trump at the White House.
Authorities later found a vehicle on fire a short distance away.
On Thursday, someone reported seeing a man with a rifle outside a Janesville elementary school.
The Rock County Sheriff's Office says they will continue following leads until Jakubowski is caught. The Janesville School District put a notice on Facebook at about 8:20 a.m. - after the school day had already started and students were at school.
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At the news conference, Janesville Police Chief David Moore said Jakubowski has had previous run-ins with law enforcement and has served time in prison, the anti-government rhetoric in the manifesto "is a new element for all of us", WISN-TV reported.
Police were forced to shut down some Wisconsin schools after the suspect allegedly made threats against them.
At the recommendation of local law enforcement, the district entered the soft-lockdown with students and staff for the afternoon. "We don't have any reason to believe he's coming here but everyone is on alert because nobody knows where he is", DeSpain said. At that scene was evidence of arson, and it appeared that the burglary and vehicle arson events were connected, deputies said.
A Janesville man is still on the run and considered armed and risky. When officials spoke to an associate of Jakubowski, they learned Jakubowski made a statement about stealing guns and about an unspecified attack.
Anyone with information is asked to call Janesville police, 755-3100.
As of Saturday morning local, county, state and national law enforcement are continuing their search for Joseph Jakubowski.