The Air Bridge Denial program became controversial after the Peruvian air force mistakenly fired on a small plane in April 2001, killing a U.S. missionary and her daughter.
After a two-year halt, the United States decided to resume the program with Colombia in 2003 following lengthy negotiations to ensure safeguards were in place to prevent future mistakes.
Bush's initial authorization for the help with the drug program would have expired on Thursday without a renewal.
Colombian President Alvaro Uribe paid a visit to Bush's ranch earlier this month, where Bush vowed to sustain funding for Colombia's fight against drugs and violence.
The United States has provided more than $3 billion in assistance to Colombia over the past five years as part of an effort to wipe out cocaine and heroin production and crush the long-running leftist insurgency.