Authorities said the system for the checks is still being developed, but the plan is for passengers carrying bags to be selected at random before they have passed through turnstiles.
Officials wouldn't immediately say how frequently the checks would occur. The checks are scheduled to begin at some stations by Thursday evening and will be occurring throughout the system by rush hour on Friday.
"We just live in a world where, sadly, these kinds of security measures are necessary," Bloomberg said. "Are they intrusive? Yes, a little bit. But we are trying to find that right balance."
Authorities said there is also a possibility that checks will be conducted on some bus and train passengers.
The explosions in three London subway stations and a bus Thursday were eerily similar to attacks exactly two weeks ago that killed 56 people including four suicide bombers.
U.S. mass transit systems remain on code orange, or high alert, since the London bombings two weeks ago, but the rest of the country is at yellow, signifying an elevated risk.
U.S. officials are unaware of any specific intelligence indicating a similar attack on the homeland, said Kathleen Montgomery, spokeswoman at the Department of Homeland Security.
She said that Homeland Security Secretary Michael Chertoff was closely monitoring events but had no immediate plans to raise the U.S. terror alert beyond current levels.
The Pentagon increased security on its grounds in response to the latest London problem. Spokesman Bryan Whitman said there was no specific threat against the building, which is adjacent to a Washington-area subway stop.