The application was filed by Michael Mannion, a British national, and one of the eye witnesses who saw the 15-year-old girl with the two accused on the night she was allegedly murdered.
Mannion said he was ready to come down to Goa to testify as a witness only if the prosecution reimbursed him for loss of his salary there and expenses incurred.
Mannion had also said he apprehended threat to his life.
"Mannion feared threat from the accused and hence had requested CBI to record his deposition via video link. He is keen to depose in the matter," his lawyer Vikram Verma told PTI.
Scarlett's semi-nude corpse was found at the famous Anjuna beach in Goa on February 18, 2008. Two persons- Samson D'Souza and Placido Carvalho - were arrested soon after on the charges of rape and murder. The duo is facing trial presently.
The case was handed over to CBI after allegations of a shoddy probe were levelled against Goa police by Scarlett's mother Fiona Mackeown.
Children's Court judge Anuja Prabhu Desai yesterday allowed the CBI application and directed CBI counsel Ejaz Khan to make necessary arrangements to record the witness's statement through video-conferencing.
The Court has so far recorded evidence of over 15 witnesses, including that of the girl's mother.