Officials said if it is allowed to cross-examine the four, there is no guarantee that the court would not ask for the cross examination of all 500 witnesses, around 50 doctors who had conducted the postmortem of all 166 victims of the massacre.
"There could be a long list of demand. Why cannot Pakistani authorities convince its court that bilateral agreement between two sovereign countries has to be obeyed by," the officials said.
Home ministry officials said they have failed to understand why the Pakistani investigators could not gather evidence in Pakistan against seven accused, including LeT commander Zakiur Rehman Lakhvi, against whom the trial is on.
The officials said the accused are in Pakistan, conspiracy was hatched in Pakistan, the terrorists were from Pakistan, the training took place in Pakistan, all logistics for the attack were gathered in that country, the boat was a Pakistani and yet they could not gather any evidence there.
"The last-mile link-up is in India. What about the first part of the whole conspiracy which was done in Pakistan," an official said.
The home ministry has asked all stakeholders -- law ministry, security and intelligence agencies -- to give their comments on Pakistan's fresh request.
"We have to see all aspects and possible repercussion. A final decision on the issue will take time," the officials said.
Pakistan had conveyed to India that it was necessary to take forward the case in the Rawalpindi court and, hence, the commission should be allowed to visit India again for cross-examination of the four.
Union Home Secretary R K Singh had earlier said India believed that the evidence collected by the commission had evidentiary value.
The eight-member Pakistani judicial commission, which included prosecutors and defence lawyers, had visited Mumbai in March.
Though they were allowed to interview the magistrate, the police officer and two doctors, the panel was not allowed to cross-examine them in line with an agreement between New Delhi and Islamabad.
The Rawalpindi-based anti-terrorism court of Chaudhry Habib-ur-Rehman had said in an order that all the proceedings and the report of the commission that visited Mumbai in March were "illegal".
The lawyers defending Lakhvi and six other accused -- all of them are in judicial custody -- had opposed the commission's report, saying it had "no legal value" as the panel was not allowed to cross-examine the witnesses during its visit to Mumbai.
The issue of the second visit by the commission had come up for discussion in India-Pakistan meeting on the sideline of NAM Summit in Tehran and in Islamabad last week.