The Advertising Standards Authority is still logging complaints and has not yet decided if it will launch an investigation. The watchdog said the majority of people complained the ad is offensive to Christians and other religions.
One of those to complain to the ASA is Stephen Green, of Christian Voice, who has challenged the ads on grounds of "truthfulness" and "substantiation", suggesting that there is not "a shred of supporting evidence" that there is probably no god.
Hanne Stinson, the chief executive of the British Humanist Association, said she could not see how the ASA could investigate complaints such as Green's
Stinson said: "I am sure that Stephen Green really does think there is a great deal of evidence for a god but I pity the ASA if they are going to be expected to rule on the probability of god's existence. If they do investigate we will be very happy to respond."
A spokeswoman for the ASA said the complaints are currently "being assessed and no decisions have been taken about what to do with them".
The campaign was launched following an appeal by a Guardian newspaper blogger who challenged readers to raise enough funds to run an ad telling people "there's probably no god" on a single central London bus route.
In the end, enough money was generated to cover 800 buses across the UK and the tube network.
The £130,000 raised by the BHA has paid for a four-week bus campaign from this week and two weeks of exposure on the tube from Monday, both through outdoor media company CBS Outdoor.
The ad features the strapline: "There's probably no god. Now stop worrying and enjoy your life".