French Prime Minister Manuel Valls said in February that Paris was "not in favour" of Merkel's proposal to set up a permanent system to redistribute more refugees around Europe.
"France has committed to take 30,000 refugees ... but no more," Valls said.
He also said that Merkel's liberal refugee policy, which brought 1.1 million asylum seekers to Germany in 2015, was not sustainable in the long run.
However despite their differences, Hollande insisted Friday that "France and Germany are working with the same spirit and the same will" on the crisis.
And Merkel said that "together, we are convinced that unilateral solutions won't help us. It won't lead to a reduction in refugee numbers."
Merkel said border slowdowns and closures had resulted in a bottleneck of migrants in Greece, overwhelming the cash-strapped country's resources.
Both leaders stressed that Russian leader Vladimir Putin confirmed his country's commitment to a ceasefire that took hold in Syria last weekend, a truce which world leaders hope will stem the flood of migrants fleeing the war zone.
"[Putin] has expressed his willingness to make sure the ceasefire is respected and that there are no attacks on civilian targets", Hollande said.