WASHINGTON, Sept. 26--Amid confusion in the Pentagon, Secretary of the Army Brucker tonight countermanded an order to Army units in the South to train for riot duty and prepare to speed to scenes of civil disorder.

The order, issued by some unnamed high source in the Pentagon, was sent out yesterday and was prompted by the Little Rock anti-integration riots which caused President Eisenhower to enforce high school integration there with the bayonets of paratroopers.

When the existence of the order was revealed today, high officials obviously felt it would lead to a belief that the Army was expecting widespread violence in the South.

There were indications tonight that one or more generals, and perhaps other officials, were being "chewed out" over the mix-up, coming as it did at a time of high tension in the South.

At the vacation White House in Newport, R.I., aides to Eisenhower were swift to say he had nothing to do with the order. Press secretary James C. Hagerty denied that the President was aware of th order and had anything to do with its issuance.

The incident came to light when a high, uniformed officer of the Army had a chat with newsmen in the Pentagon this afternoon in an effort to make his branch of the service look good.

This officer had been vague about the date of the order, saying merely that it went out "some time ago." It remained for Brucker, in his later statement to disclose that the order was not issued "before Little Rock" at all but went out yesterday, and was inspired by the troubles in Little Rock.