Wajid Shamsul Hasan told Release International he would do everything in his power to protect the rights of Christians at risk in his country.
In a surprise move, Mr Hasan came out from the High Commission to address Christians who were holding a prayer vigil organised by Release in front of the building last Thursday.
"We welcome you," Mr Hasan told the crowds. "We share your concerns, and we will do our utmost in the best possible way to provide security for the minorities and to alleviate their sufferings.
"We will take necessary measures to make sure no existing laws are abused against them."
The High Commission was presented with a petition containing more than 50,000 signatures supporting a call for the equal treatment of Pakistan's minorities.
The vigil prayed in particular for Asia Bibi, the first Christian woman to be sentenced to death for blasphemy, a charge she denies.
Bibi has appealed her sentence and is hoping that the President will be able to grant her clemency. Even if her sentence is overturned, extremists have vowed to assassinate her and a cleric is offering a reward of half a million rupees for anyone who kills her.
Militants have even threatened to blow her up in prison and her husband and children have gone into hiding.
The Governor of Punjab, Salman Taseer, was murdered by his own bodyguard after he recommended that Bibi be released and expressed his support for the repeal of the country's notorious blasphemy laws.
The High Commissioner said: "Salman Taseer's crime was defending the right of a member of the minority. We will not surrender to such blackmail, we will fight them and we will eliminate them.
"We are in the forefront of the war against terrorism. It's a war against those who abuse Islam, who declare themselves Muslims but are not. They are in my personal view more or less pagans, who have no consideration for human life."
Release CEO Andy Dipper prayed for the High Commissioner and welcomed his pledge to secure justice for Christians and other minorities in Pakistan.
He said: "We were warmly received. This petition shows many people care deeply about the situation in Pakistan and join us in calling for Christians there to be protected and given justice. Mr Hasan will represent those views at the highest levels in Pakistan."
Bishop Michael Nazir-Ali, Release patron, joined Mr Dipper in discussions with the High Commissioner.
The bishop, originally from Pakistan, said: "There was not only a receiving of the petition but an in-depth discussion of the legal and social situation in Pakistan and what can be done to ease the lot, not only of minorities, but of other people from the majority community who are in danger from some of these discriminatory laws.
"Women in Pakistan recently have suffered a setback in terms of their fundamental freedoms and we are as concerned for them as we are for other groups.
"There is greater awareness of concern in this country about what has happened in Pakistan and the deteriorating situation there."
Bishop Nazir-Ali called on Christians in the UK to pray for Pakistan.
"Everyone in Pakistan is feeling insecure. Pray that the spirit of fear that has seized the country since the murder of governor Taseer will be removed, that people will feel more secure once again," he said.
"Pray that there will therefore be justice for people to express themselves feely; for women to feel secure in terms of their personal safety."