The FAA said it will start imposing the fines because the lasers can temporarily blind pilots.
"Our top priority is protecting the safety of the traveling public. We will not hesitate to take tough action against anyone who threatens the safety of our passengers, pilots and air transportation system," said Transportation Secretary Ray LaHood in a statement.
Pilots have reported over 1,100 incidents in the U.S. so far this year, and that number is soaring as powerful, handheld lasers are sold online as tools to point out stars at night.
LAX recorded the highest number of laser events in the country with 102 reports. There were 201 reports in the greater Los Angeles area.
"People think these things are toys. They are not toys. They can be very dangerous," said FAA Administrator Randy Babbitt.
The House and Senate have passed separate measures that would make knowingly pointing a laser at an aircraft a federal crime subject to up to five years in prison, but technical and procedural issues remain to be worked out.
Dozens of people have already been arrested under state and local laws. Most were fined, but at least one California man received a prison term.
The Associated Press contributed to this story.