The team's vehicle was pelted with stones near Manikpur late night, leaving its windscreen smashed and the driver of the vehicle injured, police said.
Police officials rushed to the spot and combed the area, but the attackers had fled by then.
A case was later registered against unknown people and the circle officer of Kunda has been handed over its probe. At the time of the attack, Deputy Superintendent of Police (CBI) Surendra Singh and three other sleuths were inside the car.
The CBI team has been camping in the area for the last five days. It is trying to recreate the scene of the crime, interrogate witnesses and zero in on call details of Rajiv and Guddu Singh - close accomplices of Raja Bhaiyya.
CBI sources said that while it "was too early to conclude anything as of now, the probe was in the right direction".
An official said, "So far we have tried to piece together the jigsaw, to understand the sequence of events and the killing of Bilapur village head Nanhe Yadav, and also the mob fury thereafter."
The official explained that investigators were trying to understand the sequence that involved the firing that killed Suresh Yadav, brother of the village headman, the arrival of the police team, and the manner in which slain circle officer Zia-ul-Haq was abandoned by the police team to face the irate mob alone.
The CBI team has also tried to locate the bullet which pierced through the rib cage of Haq and exited from the chest. The circle officer's service revolver has been missing, and there is speculation that the shot may have been fired from it.
Telephone records of the accused in the four first information reports (FIRs) are also being looked into to verify their location when the killings occurred.
Raja Bhaiyya, independent legislator from Kunda, has already claimed that he was not present at the crime scene when the incident occurred. He said he was at his Kalidas Marg home in Lucknow.
The CBI team on Tuesday also got five-day custody of the accused.