The Championship club take on the Black Cats in the fourth round of the league cup at the Stadium of Light on October 30 with just 2,800 tickets handed to the Riverside Stadium outfit.
Boro are entitled to 15% of venue capacity according to Football League rules and feel hard done by that the figure they should receive has not been met.
"We are extremely disappointed with the decision," said Middlesbrough chief executive Neil Bausor.
"We believe we made a strong representation to Sunderland, together with the Football League, for a much bigger allocation and we also offered to work together with Sunderland to assist with the management of our supporters. We understand that safety of fans in sports grounds is paramount and that Sunderland know their own stadium better than anyone.
"We had hoped that Sunderland, after reviewing their risk assessment, would have made a larger allocation available to our fans. But they concluded after that review that they could not safely manage more than 2,800 Middlesbrough fans in the Stadium of Light.
"Our aim has been to give as many of our supporters as possible the opportunity to see this eagerly anticipated cup tie. We know it is something our fans feel passionately about.
"However, the League has had to accept the request of Sunderland AFC to give us a reduced allocation and, regrettably, we have had to accept it too."