"It will come up for hearing on Saturday," said his lawyer Shreyansh Mithare.
The application states that Khanna has been wrongly implicated in the case.
"After reading the charge sheet, the role which is attributed to Khanna cannot be held sufficient to implicate him in the alleged murder....It isn't the prosecution case that he has strangulated Sheena," it says.
"Prosecution has miserably failed to attribute the motive for the commission of the alleged crimes," it says.
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Khanna has also argued that statement of Rahul (the son of media baron and Indrani's husband Peter Mukerjea) has discrepancies and cannot be relied upon.
Khanna was identified in the identification parade before two persons including Rahul but bail application says the procedure was invalid because his photo had already been published in media and so this evidence is not admissible.
"(Khanna) had only come to Mumbai because Indrani had called him so that he could take Vidhie to Kolkata for a few days to spend some time with his family and celebrate the his birthday."
But he could not meet Vidhie as Indrani wanted to go to Kolkata herself first and 'inspect' his family environment to decide if Vidhie would be comfortable staying with Khanna and his family, it says.
Khanna has also denied CBI's allegation that he tried to access Sheena's email account. "On seeing the emails, he duly forwarded them to Indrani without sensing any wrong-doing," the bail application says.