The terror attacks across Mumbai are being considered a joint failure of the Customs, Coast Guard and police.
The three agencies have been jointly patrolling the seas after the 1993 serial blasts in Mumbai.
But the terrorists managed to enter with heavy arms and ammunition.
Police officials said that about 20 terrorists came through the sea route in boats. They entered the city from the shores at Sassoon Dock (in Colaba) and Badhwar Park (near Cuffe Parade) on Wednesday.
Officials added that the terrorists came from the direction of Gujarat.
Indian agencies were on Thursday questioning crewmembers of Merchant Vessel Alfa and another vessel, Matara, both reported to have come from Karachi. The terrorists disembarked from the vessel in mid-sea and got into boats to enter Mumbai.
Senior Customs officials were in closed-door meeting on Thursday following the failure to trace the terrorists while they were entering the city. Attempts to contact Customs Commissioner (Preventive) Shobha Ram turned futile.
Questions are now being raised as to why the vessel carrying terrorists was not tracked as it entered the Indian territory.