Nearly 2,000 police have been deployed to supervise Merkel's visit and authorities have banned demonstrations around the home of Prime Minister Alexis Tsipras, where the two leaders are set to meet.
Relations between Greece and Germany have calmed since her previous visits in 2012 and 2014, which were overshadowed by angry anti-austerity rallies.
But small protests by leftist parties and neo-Nazi groups were expected outside the no-go zone, while a police source said the authorities had opened an inquiry into five envelopes containing "a powder of unknown origin", which were sent to regional universities this week.
Merkel's visit is seen as a chance to leave behind a fraught period caused by tough German demands for Greek austerity accompanying EU bailouts for the country during the eurozone sovereign debt crisis.
Greece, which left eight years of bailout programmes behind last year, has also been deeply affected by the European migrant crisis in recent years.
Ahead of the trip, Merkel's spokeswoman Martina Fietz said she and far-left leader Tsipras would discuss "European and international" issues.
'Underline European solidarity'
Greek daily Kathimerini quoted Merkel as saying Greece had Germany's full support, saluting the "close ties" between the two EU states and NATO partners.
"I know that the past few years have been very difficult for many people in Greece. Europe showed its solidarity through three rescue programmes and supported Greece in its course of reforms towards fiscal and economic stability," Kathimerini quoted her as saying, hailing the "great progress" made since.
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Thanos Veremis, professor of political history at the University of Athens, told AFP that just months ahead of European Parliament elections "Angela Merkel's visit will underline European solidarity with Greece, a success for Europe".
Merkel is also due to hold talks with President Prokopis Pavlopoulos on Friday and then with New Democracy leader Kyriakos Mitsotakis, whose party is an EU Parliament ally of her Christian Democratic Union.
The leaders are likely to discuss the still thorny issue of an impending name change for Greece's neighbour Macedonia.
The former constituent part of Yugoslavia shares the name of a northern Greek province.
Tsipras and Macedonian counterpart Zoran Zaev have agreed in principle for Skopje to switch to "the Republic of North Macedonia".
But Skopje lawmakers have still to vote through a move which entails four constitutional amendments and requires two thirds support in parliament.
The European Union backs a switch, which would open the door to membership in the bloc and also in NATO.
Merkel visited Skopje before last year's referendum on the change to show support.
Yet the issue remains divisive in Greece where one party in Tsipras's coalition opposes it, threatening his parliamentary majority.
New Democracy, the main opposition party, is also against the name change
and is pushing for new elections, which are officially not due before October.