The case has come as a shock because ostensibly as per the stand taken by the company as well as its parent ministry, there may be procedural lacunae but "there is no apparent malafide in this case", he said.
While observing that "perhaps there is more to it than meets the eye," Lohani in a strongly-worded blog also said regardless of the issue, such an investigation is bound to hit the company hard.
CBI has registered a case against unknown officials of Air India, German firm SAP AG and IT major IBM in connection with alleged irregularities in procurement of software worth Rs 225 crore by the national carrier in 2011.
"Air India that has been a victim of gross indecision in recent years and only lately had started to come out of its slumber will also take a hit, I am absolutely certain, as an outcome of the unfortunate turn that this case has now taken," he said.
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"... That we should have checks and balances that are highly tilted in favour of the checks," he added.
Lohani, who took over as Chairman and Managing Director of Air India more than a year ago, has been steering efforts to revive the fortunes of the national carrier.
Known for speaking his heart, the Air India chief said the case would further strengthen the belief that following processes is important and deliverance can take a back seat.
Air India is surviving on a Rs 30,000 crore bailout package for a ten-year period which was extended by the previous UPA government.
Later in the evening, the post was removed from his blog.