Spokesman Siyabulela Qoza declined to give reasons for Sekese's special leave.
"The matter is an internal one," he said.
Sekese's deputy Gift Buthelezi had been appointed acting director general until 15 February.
Democratic Alliance MP Marian Shinn said Sekese was put on special leave because she had misled the portfolio committee about her performance contract last year.
Shinn said it was surprising that Communications Minister Dina Pule had acted only now.
"It became clear, during the two portfolio committee meetings last year, that Sekese had misled the committee about the status of her performance contract, which needed to be signed by both the minister and the director general," she said.
Shinn said the department had been "dysfunctional" for decades and the constantly changing leadership hampered its ability to focus on the country's key communications issues.
"South Africa's economic growth depends, to a large degree, on an affordable, widespread, technologically advanced communications system," she said.
"And the department of communications is just not capable of delivering this because of its lack of focus on core issues, appropriately skilled and experienced management. This latest turmoil just exacerbates that," Shinn said.
Source: Sapa via I-Net Bridge
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