Additionally, America Bikes said the opt-out provision also amounted to a funding cut.
"In the end, the full extent of cuts to biking and walking funding could be as high as 66 percent.
Boxer has defended the transportation bill from criticism, writing a letter to the Times last week to argue that the measure "actually increases the amount of financing that 'transportation alternative' projects like bicycle and pedestrian pathways are eligible for, although in some cases these projects must compete for money."
A spokesperson from the Senate Environment and Public Works Committee told The Hill on Friday afternoon that amount of money in the new transportation bill that could possibly go toward biking and pedestrian programs is approximately $3 billion higher than the total that was available in the last transportation bill, which was passed in 2005 and extended 10 times after its scheduled expiration in 2009.
The EPW spokesperson added that states are not guaranteed to opt-out of transportation alternative programs just because they have been given more flexibility to do so.
The biking provisions in the highway bill that are at issue were accepted by Senate Democrats as lawmakers negotiated were negotiating a bicameral agreement in exchange for Republicans in the House dropping a mandate that would have forced the Obama administration to approve the controversial Keystone XL oil pipeline.
The final compromise on the highway bill that was approved by Congress and signed into law by President Obama provides transportation funding through the end of the 2014 fiscal year.
-This post was updated with new information at 5:48 p.m.