The EA, which represents more than 1 million evangelicals across the UK, has said that its main concern was that exemptions to the regulations - introduced to safeguard the rights of religious groups - may be undermined by other provisions, which could lead to Christians being accused of harassment.
In particular, the EA has said that the harassment measures would aim to stop the dignity of individuals being violated, but there are concerns they could be too loosely interpreted and prevent freedom of conscience.
The General Director of the EA, Rev Joel Edwards, said: "This legislation is a symptom of a secular society in which Christianity is no longer the norm, and represents a clash of rights.
"We have to enable our members to engage as responsible and active citizens."
The EA also welcomed the anti-discrimination principles behind the legislation, and especially the regulations' focus towards preventing discrimination on grounds of sexual orientation in the area of goods, facilities and services.
The House of Lords will debate a motion from Lord Morrow to annul the SORs in Northern Ireland on 9 January, while religious groups will also rally outside Parliament in support.
The EA has been in talks with government ministers and officials during consultation in both Northern Ireland and England.
In Northern Ireland, a number of exemptions for faith groups and individual conscience have already been introduced following discussions between the Alliance, its partners and government officials.
However, Rev Edwards said it will be difficult to accurately interpret proposed exemptions in a court of law, and freedom of conscience could be eroded.
"Our members hold understandable and real concerns about the threat posed by the regulations to civic and religious liberties," he said.
"We want to hold the government to account to ensure exemptions actually work in practice, so that they don't violate individual conscience, which is a fundamental right."
He added that the Evangelical Alliance accepts the government has a challenging balancing act to accomplish in achieving a fair outcome, and is continuing to engage constructively to make sure the intended aim - respecting the rights and freedoms of all - is fulfilled.
Rev Edwards said: "We ask that those who take part in Tuesday's rally would do so in a dignified and peaceful manner."
Alistair Burt MP, an Evangelical Alliance council member, said Christian MPs at Westminster have already lobbied Communities Minister Meg Munn about the regulations and are still in contact with her as part of the consultation process.
"We are waiting to see what she proposes in detail, but hope that she will understand the sensitivity of the issue of conscience to the Christian and other faith communities," he said.
Mr Burt added that it seems clear Christians will not have a universal view about the regulations, but he hopes they will understand the need for balance and tolerance in the debate.
"I, for one, would not be able to support the regulations as drawn, but do not believe that my colleagues' faith, or that of the Minister, is in question if they do," he said.