Bunkley was forced to pay for a commercial flight and, while he arrived at the team's downtown hotel before a meeting began on Saturday evening, Bunkley was deactivated before Sunday night's game against the Colts.
The former Florida State standout could also be fined by the team.
The 14th overall choice in this year's draft, Bunkley, expected to contend for a starting job on a revamped Philadelphia defensive front, has struggled.
While the Eagles stewed over his absence, Bunkley missed the first two weeks of summer training camp in a disagreement over whether the length of his contract would be five or six years. He eventually signed a six-year deal with a maximum value of $25.1 million, including $7.46 million in guarantees. But being away from camp cost Bunkley conditioning time and also an opportunity to vie for a starting spot.
In his first regular-season game, Bunkley made a solid impression, with three tackles. But his performance has slipped since early in the season and his playing time has been dramatically reduced. Only last week, defensive coordinator Jim Johnson acknowledged that Bunkley had to start making plays to regain his spot in the regular tackle rotation.
In 10 appearances, with no starts, Bunkley has only seven tackles and has yet to notch his first sack. Over the past six games, Bunkley has just one assisted tackle.
Senior writer Len Pasquarelli covers the NFL for ESPN.com.