Officials say Benjamin Franklin High School and Science Leadership Academy, which share a campus in Spring Garden, will be closed on Thursday and Friday.
The School District of Philadelphia and the Philadelphia Federation of Teachers will meet regularly to review the progress and determine the status of re-opening.
The issues were identified during recent environmental safety walkthroughs.
Officials said there was damaged insulation material in the campus boiler room, and testing confirmed it contained asbestos.
Asbestos fibers were also detected at a low concentration in the Science Leadership Academy common area, which is currently under construction.
The campus will be closed for abatement and further testing.
The discovery comes in the wake of a $37 million construction project. The project was supposed to be completed in July, but that didn't happen.
Already this school year, the school district addressed asbestos concerns over at William M. Meredith Elementary in Queen Village.
Last month, Philadelphia Federation of Teachers called for an immediate $100 million investment to eliminate lead and asbestos from every school building after they say a longtime teacher at Meredith was diagnosed with mesothelioma, which has been linked to long-term exposure to asbestos.
The teacher has worked in district schools for three decades.
Photos obtained by Action News show apparent asbestos in the gym at Meredith.
The School District acknowledged they have many older buildings with asbestos and lead-based paint, but add they have comprehensive protocols to asses and monitor conditions to ensure students and staff are safe.
The district couldn't give an exact number on how many of its schools have asbestos or lead, but the majority of their 220 schools are over 70-80 years old.
The district reports they have completed more than 1600 asbestos remediation projects in the last three years.
This fiscal year alone, between capital and operating budgets, the district has set aside $20.7 million, specifically for asbestos abatement and lead paint repairs and assessments in schools, but district officials acknowledge they need more funding, and must prioritize issues.
If an immediate threat is identified, they say that area is shut down.
Families, media and the public are urged to monitor the District website at www.philasd.org