Palestinian sources had earlier said the representative left under pressure from the United States, which had called on Khartum to close the offices of Islamist groups.
But Ghalib Husayn, Hamas information officer in Khartum, told Reuters on Saturday that the former Hamas representative to Sudan, Jamal Isa, had merely moved to Yemen after completing his four-year term in Sudan and had been replaced.
'Nothing to hide'
"Hamas has an office here that is known to the state authorities. Nothing is hidden," he said.
"The representative of the Hamas movement has been moved to Yemen as part of an ordinary administrative procedure."
Husayn, who is also manager of al-Aqsa centre which provides information on Palestinian Islamist groups, said the new representative, Jumaa Abd al-Fattah, was not immediately available for comment.
Removal from 'list'
Washington lists Hamas as a "terrorist" group and Sudan as one of seven "state sponsors of terrorism", but recently said it would consider removing the country from the list if a peace deal to end a two-decade civil war in the south was signed.
US Secretary of State Colin Powell, who last month attended peace talks in Kenya between Sudan's main rebels and the government, said Sudan had yet to meet US demands to shut the Khartum offices of Palestinian groups Hamas and Islamic Jihad.
Sudanese government officials had previously said they would not bow to US pressure about Islamist groups.