Sharbat Gula could now face a fine and up to 14 years in jail.
Officials say she was arrested by Pakistan's Federal Investigation Agency (FIA) after a two-year probe in Peshawar, near the Afghan border.
Pakistan recently launched a crackdown against fake IDs.
Mrs Gula applied for an identity card in April 2014, using the name Sharbat Bibi. If the fraud allegations are true, she is one of thousands of Afghan refugees living in Pakistan who have tried to dodge its computerised system.
Shahid Ilyas, an official from the National Database Registration Authority (NADRA), said the FIA was seeking three staff who issued Mrs Gula's ID. They have been missing since the alleged fraud was reported.
Pakistan's Dawn newspaper reports that ID cards were issued to Mrs Gula and two men who claimed to be her sons.
A NADRA source told the paper: "They may not be her sons, but this is a common practice among Afghan refugees whereby they list names of non-relatives as their children to obtain documents."
The celebrated "Afghan girl" picture of Mrs Gula was taken in 1984 in a refugee camp in north-west Pakistan, during the Soviet occupation of Afghanistan. It led to one of the most recognisable magazine covers ever printed.
In 2002, photographer Steve McCurry tracked his subject down after 17 years of searching. At that time, Mrs Gula was living in a remote Afghan village with her baker husband and three daughters.
Pakistan's push against foreigners getting fake ID cards through fraud has detected 60,675 cards in the hands of non-nationals, officials say.
Recent UN figures show that Pakistan hosts 1.4 million registered Afghan refugees. A further one million unregistered refugees are believed to be in the country.