Schools will remain shut as Gov. Charlie Baker ordered students to stay home for the rest of the academic year and hinted classrooms could look very different in the fall as Massachusetts remains “still very much in the grips of a pandemic.”

“It’s a big decision. … It’s the right thing to do considering the facts on the ground associated with the COVID-19 pandemic,” Baker said during a briefing Tuesday at the State House. Cases of the highly infectious virus have continued to rise — now climbing to 41,199.

Schools and day care programs have been closed since mid-March in an effort to slow the spread of the coronavirus, but Baker said the state lacks guidance on how to safely return students to schools.

“Students, therefore, cannot safely return to school and avoid the risk of transmitting the virus to others,” Baker said.

When students finally do return to school, Education Commissioner Jeffrey Riley warned it could be to a very different-looking classroom. Temperature checks for students, desks spaced 6-feet apart and staggered schedules are all on the table as the state works to resume normal life without triggering a resurgence of the virus.

Riley said his department is working with public health officials “to get the best advice possible for how we bring our kids back.”

Teachers and administrators who had turned up the pressure on Baker in recent days as an initial May 4 re-opening day approached welcomed the news, even as they acknowledged the challenges of remote learning.

Jessica Tang, president of the Boston Teachers Union, said it is “the right approach to save lives” but called on the state to address “racial and economic disparities that this pandemic is exacerbating.”

Boston Superintendent Brenda Cassellius said the district “continues to struggle with disadvantaged students” in an interview on WGBH’s Boston Public Radio moments after Baker made the announcement. She said 18% of the system’s 55,000 students are still without high-speed internet access and thousands more struggle with hunger and housing insecurity every day.

Massachusetts Teacher Association President Merrie Najimy said Baker “made the right call.”

Public and private schools closed on March 17, followed by day cares a week later in an effort to slow the spread of coronavirus.

Most day cares will stay shuttered until June 29 under Baker’s new order. The governor acknowledged this has “created an unanticipated burden” for many families and parents trying to work from home.

“Maintaining this structure is the best way to keep our kids and our providers safe from the spread of this insidious disease,” Baker said.