Company spokesman Grady Semmens says the line, which delivers oilsands crude to refineries in Illinois and a storage hub in Oklahoma, has been shut as a precaution.
He says no leaks have been detected on the system, which is expected to be offline for three days while the company goes in for a closer look at the pipe.
Semmens says the pipeline was shut down Wednesday and is expected to restart Saturday.
Once the pipeline is restarted the company expects "normal operations and flows" for the rest of October, but TransCanada may have to "make up some volumes in November," Semmens said.
Heavy storms that have hit the area recently "are not helping" the operation, he said.
"But we have crews on site and will be doing excavation work to expose the pipeline so we can investigate the feature that was identified by the in-line inspection," Semmens said.
The U.S. Pipeline and Hazardous Materials Safety Administration said TransCanada reported shutting down the approximately 3,380-kilometre pipeline, which moves about 500,000 barrels of crude a day from Alberta to facilities in Illinois and Oklahoma.
Jeannie Layson, spokeswoman for PHMSA, says the possible safety issues were found on part of the pipeline that extends between Missouri and Illinois.
Layson says in an email that an agency inspector has been sent to review the test results, observe repairs and follow any necessary safety activities.
She says TransCanada hasn't reported any leaks on the system.
TransCanada has a proposal called Keystone XL to expand the system and extend its reach to the U.S. Gulf Coast.
After a series of delays, the U.S. government is expected to make a decision on the controversial $7.6-billion expansion early next year.
Pipeline opponents argue the project is unsafe because it would be carrying heavy, acidic crude oil that could more easily corrode a metal pipe, which would lead to a spill. They also say refining the oil would further contaminate the air in a region that has long struggled with pollution.
TransCanada says its pipeline would be the safest ever built, and that the crude isn't much different than oil currently arriving from Venezuela or parts of California.
— With files from the Associated Press
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