In a statement, AECL says a detailed analysis has found nine sites at the reactor needing repair.
AECL says the repairs are not a public safety issue, adding there is no threat to workers on site or the environment.
Meantime, the ministers of health and natural resources issued a joint statement saying they're disappointed the Chalk River facility won't be back online until the first quarter of 2010.
Leona Aglukkaq and Lisa Raitt say in the statement that Ottawa is working with the provinces, territories, the medical community and international partners to address Canadian medical isotope needs during this outage.
Doctors have scrambled to make do with an erratic supply of isotopes since AECL powered down Chalk River in May after finding a leak of radioactive water.