The SNP leader was accused of putting the referendum before the “ill and the injured” during a fiery First Ministers Questions session at Holyrood.
But Mr Salmond said £50 million is being pumped into address the issue. NHS staff numbers have also been protected in Scotland, despite cuts at Westminster.
Audit Scotland found that the number of patients waiting longer than four hours in A&E almost tripled from 36,000 in 2008/09 to around 104,000 in 2012/13.
It also found average waiting times have increased to over two hours, with tens of thousands of patients only being seen as they were about to breach the four-hour target set by the Scottish Government.
Labour leader Johan Lamont said the report “revealed” that the Scottish Government is to review its target of 95% people waiting less than four hours after September , which co-incides with the referendum.
“What could possibly be happening in September that matters more?” Ms Lamont said today.
“We’re not prepared to wait for his referendum before we make sure that the ill and the injured don’t have to wait for treatment.
“Is it not the case that the First Minister cares more about the constitution of the country than the health of our people?”
But Mr Salmond said a £50 million emergency care plan has already been introduced and said the target was being reviewed because the Government wants to drive it up towards 98%.
The First Minister added: “In Scotland, we have rising staff in the National Health Service, we had 127,000 in September 2006 when we took office and 135,000 at the end of last year.
“We have rising medical staff, 9,600 to 11,430, rising staff in nursing and midwifery , all made possible because we’ve protected the health service in real terms.”
Ruth Davidson said the First Minister cannot “get away from the facts.”
She added: “He missed his target for treating people in A&E, so he lowered his target - then he missed it again.”
Liberal Democrat leader Willie Rennie said the Government only “woke up” to this problem two years ago
“We’re in this position because he failed to act early enough,” he added.