There was no reaction from the court or Bowler's chambers.
The Justice Department said it would look into Rogers' concerns.
Rogers said the FBI may have been too quick to end the questioning, and criticized the judge's actions.
"That is highly unusual for a judge to intervene so hastily and make the decision not based on the facts of the interviews and the public safety exception, but what they perceived was happening based on what they saw on television," he said. "It's a dangerous precedence setting that I think we need to change and correct right away. And we still need more answers on this particular question."
Justice Department spokesman Dean Boyd also confirmed the U.S. attorney's sequence of events.
"Following the filing of the criminal complaint in this matter on Sunday, the court, that evening, scheduled an initial appearance for Monday, which it then coordinated with the prosecutors, federal defender, court reporter, U.S. Marshal Service and the hospital.
"The Rules of Criminal Procedure require the Court to advise the defendant of his right to silence and his right to counsel during the Initial Appearance. The prosecutors and FBI agents in Boston were advised of the scheduled initial appearance in advance of its occurrence," Boyd said in a statement.
Generally, suspects charged with crimes in an initial criminal complaint are to be brought before court within "one business day," even those hospitalized like Tsarnaev.
The public safety exception does not set a hard time when questioning must stop and the suspect must be taken into court, but it's generally understood to be about 48 hours. The government would have to justify holding anyone longer than that under the exception.
The court case is U.S. v. Tsarnaev (13-2106).