Air-Scotland.com was launched this week by an Egyptian entrepreneur to offer flights to six destinations in Spain.
Dhia Al-Ani, who also runs the Glasgow-based tour operator Discount Holidays, wants to turn the low-budget operation into Scotland's national flag carrier.
But the company admitted it had been surprised by the initial level of demand when the website went live.
"We had 30,000 hits in the first five minutes, which was quite unexpected," said a spokeswoman.
"We are delighted with that level of interest.
"There was a backlog with the booking system so they took it off-line to clear that backlog."
She said engineers had worked through the night and hoped to have the site up and running again on Friday.
In the meantime, the company has also been taking telephone bookings.
Low-cost service
Air-Scotland.com was set up by Mr Al-Ani in partnership with Electra Airlines, a Greek charter company privately owned by a Belgian businessman.
Two Boeings 757-200 are scheduled to start operating in March, flying from Edinburgh to Barcelona, Palma, Alicante, Malaga and Fuerteventura and from Glasgow airport to Barcelona, Palma and Tenerife.
The following month another Scottish low-cost service starts flying to mainland Europe.
Flyglobespan, a tour operator, will charter planes to fly from Glasgow Prestwick International airport to destinations in France, Italy and Spain.