It involved a surge of traffic, which resulted in many customers being unable to use the system.
Such cyber attacks - which are typically malicious - can originate from thousands of different sources, making them difficult to block.
The issue lasted for about 50 minutes on Friday.
Customers from Royal Bank of Scotland (RBS) and Ulster Bank were also affected.
"The issues that some customers experienced accessing online banking this morning were due to a surge in internet traffic deliberately directed at the website," said a spokesperson for RBS.
The bank was also the victim of a DDoS attack in December 2013, when some customers were unable to access their accounts.
After Friday's incident, dozens of account-holders took to Twitter to vent their frustration.
Some complained that salary payments were not being paid, others that the website was very slow.
The bank said there was no risk to customers and that services were now operating as normal.
DDos attacks against financial institutions are becoming more frequent.
In the United States, more than 100 banks and brokerages have been targeted by such attacks since April, according to the FBI.
In some cases, those making the attacks have threatened to repeat them, unless they are paid large sums of money.
There is evidence that some US institutions may even have paid up, as dealing with an attack can be very expensive.
The issue at NatWest is thought to be totally separate from previous problems in June, when payments were held up for several days.
At that time as many as 600,000 customers of RBS and NatWest suffered late payments.
