Incoming Finance Minister Vassilis Rapanos will also miss the summit having been rushed to hospital on Friday before he could be sworn in, complaining of nausea, intense abdominal pains and dizziness. He remains in hospital.
Government spokesman Simos Kedikoglou said Greece would be represented at the EU summit by Foreign Minister Dimitris Avramopoulos and outgoing Finance Minister George Zanias.
Samaras underwent successful surgery to repair a damaged retina and Kedikoglou said he would leave hospital on Monday.
"The orders of his doctor are for him not to travel and to stay at home for a few days," he said. The hospital said his condition was "good and improving."
A government official, who spoke on condition of anonymity, said inspectors from Greece's "troika" of lenders - the EU, European Central Bank and International Monetary Fund - were considering postponing "for a few days" a visit to Athens that was due to start on Monday.
They are expected to review the state of play in the implementation of reforms sought by Greece's lenders, given the time lost to two elections since early May.
Samaras's conservative New Democracy narrowly won a June 17 election that saw the radical leftist Syriza bloc surge into second place on a promise to tear up the terms of Greece's 130 billion euro ($162.96 billion) bailout, potentially forcing Greece out of Europe's single currency.
A coalition government of New Democracy, Socialist PASOK and the small Democratic Left was sworn in on Thursday. It said it would renegotiate the painful terms of the bailout, which is keeping Greece from bankruptcy but at the cost of harsh economic suffering.
Under a coalition program seen by Reuters on Saturday, the government will seek tax cuts, extra help for the poor and unemployed, a freeze on public sector lay-offs and more time to cut its deficit, responding to pressure from a society facing its fifth year of recession.
The program is likely to run into strong opposition from Greece's euro zone partners, notably paymaster Germany, who have offered adjustments but no radical re-write of the bailout conditions.
($1 = 0.7977 euros)
(Writing by Matt Robinson; Editing by Catherine Evans)
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