Arthur will join Juventus next season after the Italian champions reached an agreement with Barcelona for the transfer of the Brazilian international worth an initial €72m.
Arthur left for his native Brazil after Barcelona allowed their players a mini-break following the conclusion of the La Liga campaign two weeks ago but he has failed to join up with the rest of his teammates for the resumption of the Champions League.
Barcelona will face Napoli on August 8 at the Camp Nou as they seek a place in the quarterfinals, with the score poised at 1-1 after the first leg in Italy.
"What Arthur has done shows a lack of respect for his team-mates because the team wants to do well in the Champions League," Bartomeu told SPORT.
"It is not logical that playing for such an important title, a player decides to remove himself. It is unjustifiable and totally incomprehensible.
"We reached the agreement that until the Champions League ended he would continue playing for Barca, both in the league and in the Champions League. He is a player who has a certain importance in the team and who could help us.
"But he did not appear from the return of the mini-vacations. It is an unacceptable act of indiscipline. And that is why we have opened a file for him, because there is no argument to justify his absence.
"He called and said, 'I will not return, I will stay in Brazil'. It is his decision. No one has given him permission."
Arthur joined Barcelona from Brazilian side Gremio in the summer of 2018 and his style of play saw many see him as a long-term successor to Xavi Hernandez.
The 23-year-old made 44 appearances in his debut season and another 28 has been taken in this term.
