The agency submitted the charge sheet, running into 500 pages and listing 52 witnesses, before Additional Metropolitan Magistrate R V Adone.
"We have mentioned in the charge sheet that the process of separating Sheena and Rahul had started since 2009 and as they did not budge, the duo (Indrani and Peter) planned to kill her," a CBI official said.
On November 19, CBI had filed a charge sheet against Indrani, her former husband Sanjeev Khanna and former driver Shyamvar Rai for murdering Sheena and disposing of her body.
According to the official, the charge sheet filed today did not mention details of the financial transactions and the agency is likely to submit another charge sheet in future.
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In the charge sheet, CBI cited call data records it has collected to state that Peter spoke to Indrani on April 24 at around 12:24 PM for 1329 seconds and again at 1:36 PM for 242 seconds and that they exchanged messages as well.
Indrani again spoke to Peter for 924 seconds after Sheena's body was disposed of the next day.
CBI has also mentioned two mails, written by Sheena to her close friend, in the charge sheet.
In the second mail written two days later, Sheena referred to Indrani as a 'bitch' and a 'witch' saying how non-supportive she was.
Sheena was working with Mumbai Metro before she went missing in April 2012.