The 26-year old Austrian international was coming back from injury when he turned out for the Boro reserves on Tuesday but pulled up with a tight hamstring which will ensure he misses this weekend's clash with Watford at the Riverside.
Boro boss Gareth Southgate said it was a shame to see Pogatetz have another setback.
"He has done everything asked of him and is desperate to do more," said Southgate.
"He was coming in for three sessions a day, in at the training ground for an 8am session, train with the rest at 10:30am, have a break through dinner before finishing in the gym in the afternoon.
"It's in the mind and most top players are prepared to put themselves on that edge a bit more often. He falls into that category.
"I can't think of too many players at the top level who I worked with that didn't have that mindset, certainly those that had long careers with England. He's a good example to have around."