A security level of 3 is put in place when and where the risk of an attack on a UK ship is assessed to be critical, according to International Ship and Port Facility (ISPS) security code.
The UK official told CNN on Friday that media reports about the threat level being raised to its highest level for ships in the Middle East were accurate.
CNN understands that British officials considered a variety of sources -- including open source information, intelligence, previous behavior, recent events and international partnerships -- before making the decision.
"Information from all of those sources enables Her Majesty's Government to make rounded decisions that protect UK and/or allies interests," a UK security source told CNN.
Britain is also sending the warship HMS Duncan to the Gulf to maintain the UK's maritime security presence there, while another ship, the HMS Montrose -- which was involved in the incident with Iranian ships on Wednesday -- undergoes maintenance and a change of crew, the Ministry of Defense told CNN in a statement Friday.
"This will ensure that the UK alongside international partners can continue to support freedom of navigation for vessels transiting through this vital shipping lane," the statement added.
The HMS Duncan will deploy to the Gulf after being sent to the Black Sea earlier this week to lead UK involvement in NATO war games.
Britain is "not seeking to escalate the situation with Iran," said UK Foreign Secretary Jeremy Hunt after the deployment was announced.
"None of us are looking for a conflict. And we all have a responsibility to protect shipping, this is a time for cool heads," he said in a press briefing Friday.
"We want to do everything we can to make sure that we don't have an unintended escalation which could be very dangerous to the world," Hunt added.
to raise the threat level comes as Iran has threatened to retaliate against the UK after British commandos seized an Iranian tanker
off the coast of Gibraltar last week. The UK said the tanker was seized because it was in violation of EU sanctions against shipping oil to a port in Syria, which is where the UK said the Iranian tanker was heading. Iran has denied the tanker was going to Syria.
A day after the threat level was reportedly raised, armed Iranian boats unsuccessfully tried to intercept a British oil tanker as it was crossing into the Strait of Hormuz. The HMS Montrose was escorting the tanker then leveled deck guns at the Iranian vessels, turning them away.
The director of policy at the UK Chamber of Shipping, David Balston, confirmed to CNN that the British Department for Transport (DfT) issued the warning to UK-flagged vessels "on a one to one basis" several days ago.
The increased threat level requires ships to take extra security precautions, which are confidential, Balston said, adding that the measures would include advice about which routes are navigated.
The one-to-one communications take place because the DfT, often working with the Chamber of Shipping, issues threat warnings to companies and vessels which are potentially vulnerable, rather than sending out a blanket order to the entire industry. Threat levels are also issued by individual nations to the ships of those nations only, Balston said.
A DfT spokesperson told CNN in a statement: "The Department for Transport, as competent authority, regularly provides security advice to UK and Red Ensign Group Shipping on how they should operate in areas of high risk."
CNN has also reached out to the UK Ministry of Defense for comment.
Laboratory testing has confirmed Grace 1, the Iranian tanker seized by the British navy on July 4, was carrying 2.1 million barrels of light crude oil, Gibraltar's Chief Minister said Friday.
"We will not allow Gibraltar to be used or to be knowingly or unknowingly complicit in the breach of EU or other international sanctions or for any of the matters which our laws prohibit," said Chief Minister Fabian Picardo in Parliament.
The ship's captain and chief officer were arrested Thursday on suspicion of breaching EU sanctions relating to Syria, according to a statement from the Gibraltar Police.
UK Foreign Secretary Hunt said Friday the Royal Navy seized the tanker because it was a "clear breach of sanctions."
However Iran has demanded the ship's immediate release, insisting the ship was not bound for Syria and was not breaching EU sanctions.
Iran's foreign ministry spokesman Abbas Mousavi warned the UK not to "enter into a dangerous game under the influence of the Americans with no end in sight" in a Friday interview with state-run IRNA, according to Iranian state-funded Press TV.
Mousavi said there are no ports big enough to accommodate the super tanker in Syria.
CNN's Barabara Wojazer, Jennifer Hauser, Jack Guy, Zahid Mahmood, Sarah Dean and Lauren Said-Moorhouse contributed to this report.