The company has also increased its guaranteed contribution to Queensland's Disaster Relief Fund to $AUD3million, a 50% increase on its initial $2million pledge.
The donations follow a six-week fundraising campaign that was initiated on January 18, in the aftermath of the south-east Queensland floods.
In announcing the campaign, FLT managing director Graham Turner said the company would donate $10 for every ticket issued by its Australian leisure travel shops between January 18 and February 28.
Today, Mr Turner said FLT had easily surpassed its initial $2million target, which would allow it to provide further financial support to the people of Queensland and Christchurch.
"We have been extremely fortunate in that none of our staff members have been injured, but our people and our customers have been directly affected by these tragic events," he said.
"While we initially focused on raising funds for those affected by the Queensland floods and cyclones, we believe it is appropriate to now extend our support to New Zealand in light of Tuesday's earthquake.
"Thanks to our people's efforts and our customers' support over the past six weeks, we are now in a position to increase our contribution to the Queensland Premier's fund by 50% and, at the same time, donate an additional $NZ1million to help those affected by the earthquake.
"In total, we now expect to donate in the order of $AUD4million when our campaign finishes at the end of this month. The final donation is not capped."
FLT is one of New Zealand's largest travel agency groups and has about 170 businesses throughout the country.
Seventeen shops in and around Christchurch were affected on Tuesday.
Flight Centre New Zealand will also create a separate fund to help staff members.
Up to 70 shops in south east Queensland were temporarily closed after last month's floods, while the company's head office in Brisbane's Queen Street was lightly staffed for a day.