The popular 32-year-old Argentinian has made just one league and two cup appearances this season and has undergone surgery to try to solve the long-running problem.
However, manager Tony Mowbray revealed that Arca is still struggling with the problem and is set to miss the remainder of the campaign.
"I don't think Julio is going to make the rest of the season," he said. "I had a chat with him today and he's had a setback with his toe.
"He had trained for the last three or four days and looked really good in training.
"Julio is a quality footballer with the ball at is feet and he had pepped training up. But after this setback I'm not anticipating seeing him again this season.
"It's a shame for him and for the club. We wish him well and if we don't see him again it will be a disappointing end because he's out of contact in the summer."
Midfielder Arca is Boro's longest-serving player and has made 155 starts and 30 substitute appearances in all competitions since joining Boro from Sunderland in 2006, scoring nine goals.
In total he has made 320 starts and 42 sub appearances in English football, with 32 goals to his name.
He signed a new two-year Boro contract at the end of the 2010/11 season after being voted the club's Player of the Year.