"Very unfortunate developments, this should not have happened at Infosys," Deshpande said when asked about the recent events at the city headquartered company.
"I can understand transparency is very important. If there is no transparency there are ways to find out the truth, but unfortunately, according to me, investors' confidence and shareholders' confidence have been shaken," he told reporters.
"Infosys is the pride of the country, it is known to the entire world. We are all proud of Infosys. I can only say such developments are unfortunate," he added.
Last Friday, Sikka, the first non-founder CEO of Infosys, resigned from the company following months of acrimony with high-profile founders, led by N R Narayana Murthy, citing "malicious" and "personal attacks" on him.
While Sikka did not name Murthy for his exit, the board of the US$10 billion firm blamed the founder for "continuous assault" through "factually inaccurate" and "already-disproved rumours" for the resignation of the CEO.
Murthy, however, maintained that his only concerns were the lapses in corporate governance standards, something that Infosys was admired for at one point.
Sharp decline in Infosys share prices following the developments has wiped out Rs 34,000 crore of investors' wealth in the last two days.
When asked about reports that Nandan Nilekani is likely to return to Infosys, Deshpande said he would not like to comment on it, and it is left to the decision of the board, founders and shareholders of the company.
Nilekani, one of the co-founders of the company had joined the Congress party ahead of 2014 Lok Sabha polls. He had also contested and lost the election from Bengaluru South constituency.
Noting that the developments at the company were not healthy, Deshpande said, "founders have struggled for the company, at the same time shareholders have fully cooperated. Vishal Sikka also has good reputation. These things should have been sorted out in-house".
"I think, still time is there. I am confident that they are all people with rich experience, good people. The board, founders and shareholders will come under one roof to resolve this issue," he said.