The excerpts, released on Monday, excluded the names of gunman Omar Mateen as well as Abu Bakr al-Baghdadi, the leader of the so-called Islamic State (IS).
Mateen, who killed 49 people at a gay Orlando nightclub, described himself as an "Islamic soldier" and pledged allegiance to al-Baghdadi during his phone calls to authorities.
But in the first version of the transcript, any reference to IS or their leader was removed.
For example:
Police: What's your name?
Mateen: My name is I pledge allegiance to [omitted].
The decision to omit the names sparked outrage among Twitter users including US House Speaker Paul Ryan.
The Wisconsin Republican denounced the decision to redact as "preposterous" and called on the Obama administration to release the full transcript "so the public is clear-eyed about who did this, and why".
"We know the shooter was a radical Islamist extremist inspired by Isis. We also know he intentionally targeted the LGBT community," Mr Ryan said in a statement, referring to IS.
Other users expressed outrage over the decision to remove IS from the text.
The Department of Justice released a statement later on Monday defending the redaction.
Officials said they wanted to remain sensitive to the victims, their families and the ongoing investigation, while also not providing "the killer or terrorist organisations with a publicity platform for hateful propaganda".
"Unfortunately, the unreleased portions of the transcript that named the terrorist organisations and leaders have caused an unnecessary distraction from the hard work that the FBI and our law enforcement partners have been doing to investigate this heinous crime," the statement said, before releasing the full transcript of Mateen's first 50-second phone call.
The other calls he made were not released.
Mateen first called a 911 dispatcher about 30 minutes after he began shooting. During the call, Mateen spoke Arabic and praised "God the Merciful".
In a later phone call, he told a negotiator to tell America to stop bombing Syria and Iraq and that was why he was "out here right now", according to the FBI transcript.
Mateen also told negotiators he had an explosive vest similar to the kind used by terrorists "in France," making a reference to the November terror attack in Paris. But no vests were found.
"[Mateen] does not represent the religion of Islam, but a perverted view," said Ron Hopper, the FBI assistant special agent in charge.
"Part of the redacting is meant to not give credence to individuals who have done terrorist attacks in the past," he said. "We're not going to propagate their violent rhetoric."

Lodsys has said that Rovio and other developers violated its patents with games on Apple's iOS platform and Google's Android.
Lodsys is embroiled in lawsuits with other big technology companies, including Apple.
Rovio said it had not received any direct contact regarding the complaint.
"As soon as we receive more information we will take appropriate action," a spokesperson said.
Angry Birds is one of the most popular game applications.
Rovio marketing chief Peter Vesterbacka said last week that the game had surpassed 300 million downloads.
Lodsys, a company that licenses patents but does not have any other business, added five new defendants to a suit filed in May with a US district court in Texas.
Along with Rovio, it named Electronic Arts, Take-Two Interactive which makes Grand Theft Auto, Atari and others in the list of companies it says are violating its patents.
Take-Two declined to comment. Electronic Arts and Atari were not immediately available for comment.
The Department of Justice has re-issued a fuller transcript of one of the Orlando gunman's 911 calls without redactions, after facing a wave of online backlash for omitting certain words.
[NEXT_CONCEPT]
Rovio, the Finnish maker of the Angry Birds game, is being sued by a licensing company for infringing its patents.