Several trains are set to be affected on Saturday as the rail operator seeks to assess the extent of the problem, which does not affect high-speed X2000 and double-decker trains.
Many passengers were transferred to coaches on Friday afternoon as SJ launched an inspection of its rolling stock and cracks were found in a couple of wheels.
"Two wheels of around 3,000 checked were shown to have cracks. We take this very seriously and have now decided to take all the trains out of service," said Elisabeth Lindgren at SJ on Friday afternoon.
In order to cope with demand for trains from Stockholm to Uppsala, SJ hired in trains from local transport operator SL.
The inspection is a result of SJ's own inspection work following the accident in Skotterud, Norway two weeks ago.
The accident was initially considered to have been caused by a wheel fault which had emerged as a result of general wear and tear.
SJ's inspection of its rolling stock is expected to be completed during next week. The aim is to be able to operate almost normal services on Saturday as passenger numbers drop.
On Friday evening SJ said that five departures would be affected on Saturday - two between Karlstad and Stockholm, two between Kalmar and Gothenburg and one between Hallsberg and Stockholm.
But on Friday the interruption hit 4,000 of SJ's around 100,000 customers with the cancelled trains leading to hastily rearranged travel plans.