Khawaja was also rested from the Australia's squad touring New Zealand for the Chappell-Hadlee ODI series, which the home side went on to win by 2-0. He was instead send to Dubai for a pre-tour training camp for the Border-Gavaskar Test series in India.
Later, the 30-year-old sat out in all four Tests against India, with the selectors choosing Shaun Marsh in his middle-order role.
"The most frustrating thing for me was not to play those three ODIs in New Zealand. Getting pulled out from them to come to Dubai to prepare for 10 days and then not play the first Test. So I actually miss out on the one-day matches for Australia. For me that was the tough part. I got pulled out of that series to prepare for India and then not playing was a bit hard," ESPNcricinfo quoted Khawaja as saying.
Khawaja said that although he sort of had an idea that he would not play in the opening Test against India because of his poor performance in the tour match, he was quite disappointed to miss the rest of the four-match series.
"Maybe when I younger I would have been frustrated [at missing out on the Tests in India]. In saying that obviously I would have loved to play in that Test series, [and] when I didn't get to play in that first Test I was a bit frustrated," he said.
"I sort of had an idea I was not going to play in that first Test after I didn't get a run during the tour match. We played brilliant in that first Test match and we won. I was frustrated at the time, not so much because I didn't play in that Test match -- I understand the selectors, Boof [coach Darren Lehmann] and picking the best team and what was going on and I just want Australia to win," Khawaja added.
Khawaja, however, said that he felt much better after discussing the situation with coach Darren Lehmann. The batsman revealed that following the discussion with the coach he had made the mind to do best for his country and be fully read in case the opportunity did come up to him.
"To Boof's credit I had a chat to him about all that stuff and he came up to me and he actually knew where I was at in that things had not worked out, not being able to play the ODIs and come early to India, he knew exactly where I was coming from," he said.
"Once I chatted out to him it helped me quite a bit. He has seen it all, he has seen the ups and downs so after I had that discussion with him I was fine. I was just like 'there are few more ODIs coming up that I can look forward to'. After that chat I was fine and just trying to do the best for the team and be ready in case the opportunity did come up," Lehmann added.
The 2017 Champions Trophy is slated to be held in England and Wales in June. (ANI)