The result now brings the top of the Serie A much closer.
There was nothing about the result that Atalanta did not deserve and they were full value for their win.
Early pressure by Atalanta had Inter playing very much off the back foot for most of the match. The match was over as a contest just after the half hour mark. Sergio Floccari who latched onto a poor clearance with a powerful shot scored the first goal. Cristiano Doni added two more. The first came from a direct free kick and the second with his head from a Jaime Valdes cross from the left. Zlatan Ibrahimovic scored a consolation goal in the ninetieth minute.
ROME (AFP) - Inter Milan coach Jose Mourinho described the 3-1 mauling at Atalanta as the defending champions' worst performance of the season.
Inter were woeful in the opening 45 minutes as their hosts totally out-played them to turn around at the break with a 3-0 advantage courtesy of a brace from veteran Cristiano Doni and Sergio Floccari's 10th league goal of the season.
The former Chelsea boss rung the chances and threw on forwards Adriano, Victor Obinna and Luis Figo to try to rescue the match, but had only Zlatan Ibrahimovic's poke from a yard out in injury time to show for their efforts at the final whistle.
"That was our worst performance of the season, you could compare it with our match in Cyprus in the Champions League (a 3-3 draw at Anorthosis Famagusta)," said Mourinho.
"I can't explain my team's first half hour. When we lose I prefer to speak about how well the other team played but we played so badly in the first half that I prefer to say that we brought this result on ourselves.
"I will accept all the criticisms you want to direct at me. The press can use all the adjectives they want and I won't complain.
"It was a disaster. Against Cagliari (a 1-1 home draw a week earlier) it was the first match back after the winter break which is never easy but we saw an emotional reaction (from Inter when they went 1-0 down) from a team that wanted it.
"But even someone who doesn't know football could see that we didn't have the aggression to win the ball or the desire to press, we didn't have the right attitude.
"If the team didn't manage to do that then the coach is at fault for not being able to make them do it. There were 30 minutes that you can't explain in which we conceded stupid and ridiculous goals.
"One of my players (Maxwell) put the ball at the feet of Floccari, who had his back to goal but our defender (Ivan Cordoba) let him turn and shoot.
"The whole week we spoke about Doni and how he plays in a certain area and is good in the air, but he found space on his own between two defenders.
"The coach wasn't able to make a 34-year-old centre-back with 15 years of experience understand that you can't let a striker with his back to goal turn and shoot.
"My team played really badly but I'm the coach so it's my fault."
However, Mourinho said he expected something positive to come out of this defeat, only Inter's second of the season in the league and the first time in Serie A since May 13, 2007 in a 4-3 win over Lazio that they have conceded three goals.
"I like the difficult moments and a dreadful one such as this can be positive, it will serve to change something, mainly the right attitude which simply wasn't there."
Inter have six points less than they did at the same stage a year ago under Mourinho's predecessor Roberto Mancini, something which the Portuguese refused to talk about.
"All I can say is that every other team in Serie A would be delighted to be in the same position as us at the halfway point of the season."
Inter are top with a three-point lead over Juventus and six ahead of bitter city rivals AC Milan in third.