Sec. of State Condoleezza Rice has apologized for the breach.
The breaches raises questions about whether the passport peaking was politically motivated.
The State Department has called the breach of passport files "inappropriate curiosity." In fact, Hillary Clinton's file was reportedly accessed briefly by an intern in training last summer, who was immediately told to find a different practice file.
The McCain breach was earlier this year, in the heat of the primary season, as were all three forays into Obama's file. That could be coincidental, except for the fact that Obama did live in Indonesia, a Muslim country, as a child. And that could have sparked some curiosity about his travels as an adult.
"It is deeply disturbing. This is something that has to be investigated diligently and openly," Obama said.
Obama, the Democratic presidential frontrunner, received an apology by phone Friday morning from Condoleezza Rice.
" I told him that I was sorry, that I myself would be very disturbed if I had learned that somebody looked at my passport file, and therefore, I will stay on top of it and get to the bottom of it," she said.
The Illinois senator's passport file was breached three times this year in the heat of the primary season. That is a red flag, according to a former inspector general at the State Department who is now a private security analyst.
"These files were accessed close to primary dates. The fact that, according to the State Department anyway, senior management learned about it from a reporter yesterday suggests a political motive. Certainly, that is one of the questions," analyst Clark Kent Ervin said.
The State Department admits the passport files of the other president candidates, Clinton and McCain, also were breached in the past year, one time each.
Two contract employees have been fired, so far. One has been reprimanded.
"One of the same people who accessed Senator Obama's file, also accessed Senator McCain's passport file," said State Department spokesperson Sean McCormack.
The breach brings back memories of a similar breach in 1992 when Bill Clinton was running for president.
"The State Department was not only rifling through my files but actually investigated my mother, a well known subversive," President Clinton said in 1992. "It was would be funny it wasn't so pathetic."
"One of the things that the American people count on in their interactions with any level of government is that if they have to disclose personal information, then it stays personal and should stay private," Obama said.
One of Obama's political allies, Chicago congressman Jan Schakowsky, sent a letter to Rice Friday afternoon asking why contract employees who work for private companies are given access to sensitive passport data? Why the breaches weren't made public sooner? And why none of the supervisors who discovered the breaches in the first place have been disciplined for failing to pass the information on the their bosses?
The story about the file breaches broke in a Washington newspaper Thursday night.