While Sri Lanka Cricket (SLC) had arranged the side nets for the training session, Pakistan wanted the centre wicket where a softball game was in progress.
After failing to persuade the Sri Lankan authorities to stop the game, the Pakistan players returned to the team hotel.
"We went to the ground as scheduled in the morning but found out some others were using it and we had no other alternative but to return to the hotel," Pakistan team manager Zaheer Abbas told AFP.
"After we contacted SLC we were given a different venue to practice in the afternoon," Abbas said.
While the Pakistan cricketers hung around for about 40 minutes, some of the players, including bowling coach Waqar Younis, sent down a few deliveries for the locals.
SLC officials said the inconvenience was caused by miscommunication.
"We had earlier allocated the side nets for the Pakistan team, but subsequently they requested for the centre wickets and we couldn't arrange that at the last moment," a spokesman said.
Pakistan arrived in Colombo on Sunday and will play two Test matches. The first one-dayer begins Friday at Colombo's R. Premadasa Stadium.