The retail giant acknowledged it was an "emotive topic" but said its policy had to evolve with changing circumstances.
From this week, sick pay cuts will be implemented at Wessex Water and in the US several major companies have started penalising unjabbed workers.
It comes as firms struggle with mass staff absences and rising costs.
At Ikea unvaccinated workers, who do not have mitigating circumstances, who test positive will be paid in line with company sick pay.
Unvaccinated workers, without mitigating circumstances and required to isolate owing to being identified as a close contact, could now receive as little as £96.35 a week - the Statutory Sick Pay (SSP) minimum.
Average wages at Ikea are between about £400 and £450, depending on location and, as is the case at many companies, staff get enhanced sick pay. The move was first reported by the Mail on Sunday.
Ikea, which employs about 10,000 people in the UK, said in a statement: "Fully vaccinated co-workers or those that are unvaccinated owing to mitigating circumstances which, for example, could include pregnancy or other medical grounds, will receive full pay.
"Unvaccinated co-workers without mitigating circumstances that test positive with Covid will be paid full company sick pay in line with our company absence policy.
"Unvaccinated co-workers without mitigating circumstances who have been identified as close contacts of a positive case will be paid Statutory Sick Pay."
In England, people who are vaccinated with at least two doses need not self-isolate if they have been in close contact with someone infected with Covid. Unvaccinated people contacted through the government's test-and-trace system must still isolate by law.
Many companies complained of labour shortages throughout 2021, and now are seeing mass absences due to the more infectious Omicron Covid strain.
Prime Minister Boris Johnson repeated on Monday that the data continued to show those people most seriously affected by Omicron remained the unvaccinated.
Wessex Water's sick pay rule change comes into force this week.
Any employee without at least one Covid-19 vaccination - who does not have a valid medical reason - or does not have a confirmed vaccination appointment, will get only statutory sick pay if required to self-isolate due to close contact with someone testing positive.
A Wessex Water spokesperson said absences have soared this year: "The vast majority of our workforce has been vaccinated and it's important as a company providing essential services with key worker employees, the remainder get vaccinated to protect themselves, customers and their colleagues.
"Absences due to Covid have doubled in the last week, so we need everyone to be available so we can continue to provide uninterrupted essential water and sewerage services."
The company said that throughout the pandemic it had not furloughed staff and those self-isolating had received full pay.
Last year, supermarket Morrisons cut sick pay terms, while several companies, including banking giant Citigroup, introduced a "no jab, no job" policy. Delta Airlines imposed a surcharge on unvaccinated staff members of its healthcare plan.
Ben Willmott, head of public policy at the Chartered Institute of Personnel and Development (CIPD), told the BBC there were pros and cons with changing sick pay terms for certain workers.
It could encourage staff to get vaccinated, but others might be less likely to test themselves or self-isolate because they could not afford time off work at the statutory rate of about £96.
His organisation's official guidance was not to differentiate between employees, as the consequences could be complex and there were potential legal problems.
"You would have to manage it on a case-by-case basis because of legal risks," Mr Willmott said.
Earlier this month, David Josephs, boss of food importer and retailer All Greens, told the BBC that staff at some firms were ignoring Covid rules for financial reasons.
"We know that in our sector a lot of staff do not get paid sick pay. Ours do - but staff who are on limited contracts or on minimum wage cannot afford to be off work," he said.
Employment lawyer Sarah Ozanne, of CMS, also warned of complex legal issues and said striking the right balance was difficult.
"This action [by Ikea] seems more of a reaction to staff shortages and how to manage them than any intended 'discrimination' of the unvaccinated," she said.
"But employers should consider whether their actions are proportionate as a means of achieving the aim of getting employees back into work."