The Boston Police Department (BPD) confirmed that a male suspect was in custody in relation to the incident, which comes less than a week before the event, and that the bags had been destroyed.
Pedestrians and motorists were told to avoid the area near the finish line, with the BPD stating that the bomb squad had been destroyed as a precaution.
"BPD confirming that the unattended bags at the Finish Line have been disrupted for precautionary reasons," the BPD said on their Twitter account.
"BPD confirming a male suspect in custody in connection to the unattended backpacks found at the Finish Line."
It comes a year after three people were killed and more than 250 injured after backpack bombs exploded near the finish line of the 2013 Boston Marathon.
Boston commemorated the one-year anniversary of the attack by paying tribute to those who died on Tuesday.
The Boston Athletic Association prohibited backpacks and bags along the course this year and more than 3,500 police officers are due to patrol the 2014 marathon.