Ms Pillay said: "It's an act of attempted assassination so he needs to be protected immediately."
Mr Shauketaly, 52, who holds joint British and Sri Lankan citizenship, is a reporter for the Sri Lankan newspaper The Sunday Leader.
Ms Pillay said "I'm deeply disturbed by this particular shooting because it's a journalist and he's attached to a newspaper that's known to be critical of the government - particularly on accountability and in justice issues - which are issues that I cover. And I will be reporting to the Human Rights Council my concern over extra judicial killings, abductions and this kind of treatment and suppression of freedom of expression."
The newspaper's editor Sakunthala Perera said the journalist was shot while he was on the telephone discussing a story due to appear in this week's edition.
Police said three men broke into his house and opened fire on him while he was in his bedroom. The journalist, whose family live in Colywn Bay in Wales, was rushed to hospital with bullet wounds in his neck.
Time to 'demonstrate' integrity
Though he has miraculously survived, Mr Shaukatally is undergoing further tests in intensive care ahead of surgery. In 2009 an editor from the same newspaper was killed and other members of staff have also been attcked. No arrests have been made to date.
Today the Sunday Leader's website reported that Sri Lanka's Presdient Mahinda Rajapaksa has ordered a special investigation into the shooting incident.
However, when asked about suggestions that the government could have been involved in the shooting, Ms Pillay told Channel 4 News: "That's why there has to be a proper investigation before we can conclude that. In the meantime it's law enforcement that has to provide him protection. And it would demonstrate on the part of the government that they care if one of their citizens is fired upon. Everybody should care (about) who are the people who are going around shooting other people. This is what law enforcement is about.
"The Sri Lankan government swears by the integrity of their army and their police, well it's time they demonstrated that. These institutions built into the democracy must now begin to work properly and this is an immediate instance where they can demonstrate that. "
She said Sri Lanka must provide a credible investigation involving the civil society, because "if it is done by the government or the police themselves they do not enjoy the confidence of the people at this stage."
Human rights record
Sri Lanka's rights record has been subject to criticsim over alleged excesses during the military's final phase in defeating Tamil Tiger seperatists. Rights groups say the military killed thousands of minority ethnic Tamil civilians in the final weeks of the conflict.
Ms Pillay praised Channel 4's investigative report, Sri Lanka's Killing Fields, on the last few weeks of the Sri Lankan civil war, broadcast in 2011.
She said: "Let me say how much Channel 4's information is appreciated because you have brought this to the fore. I myself mandated by the Human Rights Council have been filing reports on the human rights situation in Sri Lanka - we will be reviewing that again in March, but I have consistently called for a credible international investigation particularly of the occurrences in the last few days of the conflict."
She added that she was frustrated by the Sri Lankan government's lack of investigation, with offers of UN help, to establish what happened at the end of the country's civil conflict.
The Sri Lankan government has rejected allegations of mass killings and has been dismissive of Ms Pillay's calls for investigation, alongside her calls for the demilitarisation of the Vanni region.
But Ms Pillay insists: "We want to provide them with expert investigative assistance, we are ready to provide this kind of assistance and I'm really disappointed it has not been taken up."
She added: "It's particularly bad because this was government forces firing on civilians indiscriminately - they were shelled and the normal responsibility of governments is to protect people - not to kill them."
Criticism was also levelled at the UN which was in Sri Lanka at the time of the alleged atrocities and whose people were withdrawn.
She said: "I think that is deeply disturbing because it's a repetition of the criticism that was levelled against the United Nations during the Rwandan genocide and there was a report done after that with recommendations.
"Now, to the credit of the secretary general he set up the Petrie Commission to look at the UN's failures in handling the Sri Lankan conflict and I very much encouraged that, I've read the report and I'm urging now the United Nations to take steps to come up with action plans to implement those recommendations so that the United Nations doesn't repeat these kind of failures."