Immigration Minister Amanda Vanstone faced fresh calls to stand down after a Commonwealth Ombudsmans report on Thursday described as "catastrophic" her departments handling of the Vivian Alvarez Solon case.
Howard said while Alvarez Solon deserved an apology, Vanstone had not personally known about the mistaken deportation and the subsequent cover-up.
"If somebody in a remote part of a department makes a mistake, to automatically say that because of that mistake the minister has to resign would mean that to be quite frank, ministers would be resigning all the time through no personal failing of their own," he told commercial radio.
Alvarez Solon was deported as an illegal immigrant in July 2001, even though she was a naturalised Australian citizen and was suffering major injuries from an accident at the time.
The Ombudsmans report by former Victoria state police commissioner Neil Comrie found at least three immigration officers became aware of the mistake in 2003 and 2004 but made no attempt to rectify it.
Alvarez Solon, who has two Australian-based children aged 17 and nine, was eventually discovered in a Manila hospice last May after media coverage of her case.
The case came to light after it was revealed another Australian, German-born Cornelia Rau, was wrongfully imprisoned for 10 months as an illegal immigrant.
Since then, the immigration department has admitted wrongfully detaining more than 200 people who were in the country legally and revealed many had received compensation packages in return for not going public with their cases.