The line is expected to stay shut for a “significant” period while repairs are made to the river bridge, Network Rail said.
Extra checks are also being made on similar bridges after an 80ft (24m) long section of the parapet/side wall fell away.
In August, three people were killed when a ScotRail train hit debris washed onto tracks following heavy rain.
Today’s damage is believed to have been spotted by a member of staff on a ScotRail train shortly before 10am
Network Rail Scotland said it was a structural fault and not caused by a landslip.
It described the damage as “extensive” and would take a significant period to repair despite engineers working round the clock.
A Network Rail spokesperson said: “The line is currently closed while our engineers repair a damaged side wall on a bridge between Carmont and Stonehaven.
“Specialist structural engineers are currently assessing the fault and putting plans in place for its repair.
“Our engineers will be working around-the-clock to complete this work as quickly as possible.”
The engineers are likely to investigate whether recent extreme weather was a factor.
The official rail information service JourneyCheck reported: "Due to urgent repairs to a bridge between Laurencekirk and Stonehaven all lines are closed."
The line is also used by LNER trains between Aberdeen and London and CrossCountry trains between Aberdeen and the south west of England.