Despite efforts by opponents to obtain a temporary restraining order, work crews excavated an area in Fallbrook believed to contain ancient members of the San Luis Rey Band of Mission Indians.
The tribe sued San Diego County and Pardee Homes over the construction of a new road, which runs northeast of Highway 76 and Interstate 15.
The project will include an 844-home subdivision and satellite campus for Palomar College.
Before 7 a.m. Thursday, tribe representatives said crews excavated the area where known sets of remains were buried.
"Without any regard for our ancestors or the law, they came and just pushed dirt right over the top," said James Trujillo with La Jolla Band of Luiseno Indians.
The tribes claim crews started work around 6:30 a.m. before American Indian monitors were on site to protect the areas in question.
"What has happened today is heartrbreaking to me. Since being here since a year ago, trying to preserve and protect our ancestors, it's just like a slap in the face," said Cami Mojado an onsite monitor.
The road was approved by all necessary agencies according to a spokesperson with Palomar College and on the day a temporary restraining order was requested, developers had no plans to stop.
That TRO was scheduled to be reviewed Tuesday but the review was delayed again.
Palomar College released a statement late Thursday saying they are aware of the sensitive nature of the project but will continue work on the road as approved by all necessary agencies.
The statement did not address what happened at the site Thursday morning.