She is on a whistlestop tour of Europe this week as part of what some have called a "charm offensive" to help restore confidence in the future of the EU.
Speaking at a joint press conference with Estonian Prime Minister Taavi Rõivas, Merkel said, "This is a phase of listening, of understanding and learning from one another so that we can really understand and develop a new balance within the European Union of 27 members that will remain…we have to consider what are our priorities are going to be and where we want to continue our efforts."
Her visit to Estonia is part of a wider European tour to prepare the groundwork for a key EU summit on the future of the EU in Bratislava on 16 September.
She also said, "We have enough to do among the 27 (remaining countries), looking at the questions about the future, so that we can afford to let Britain take the time it wants to clarify how it wants to shape the future relationship."
The German Chancellor, who had similar meetings with the leaders of France and Italy on Monday, also mentioned she would consider setting up joint military units with Estonia, as Germany has done already with other countries like France.
This might require the participation of other countries besides Estonia given the disparate sizes of the two militaries, she added.
Elsewhere, Norway says it wants to maintain close ties with the UK but admits that after the outcome of the EU referendum on 23 June this may take time.
On Wednesday, Elisabeth Aspaker, Norway's Minister of EEA and EU Affairs, said, "We want to maintain at least as near a relationship with Britain as we have today.
"Our goal is to have a well-functioning solution with Britain in place as soon as possible. But we must be prepared to the fact that it could take a long time and that it may not be in place the moment Britain leaves the EU."
Meanwhile, the CPMR, a Rennes-based maritime organisation, has called on the European Commission to put regions and citizens "at the heart of plans to reshape and rebuild the European project, particularly during this period of crisis."
CPMR Vice President Enrico Rossi, President of the Tuscany region, said that the European project has been thrown into turmoil by the UK vote to leave, but with the support of regions the EU "can help rebuild a better future."
Rossi called on the Commission to renew cohesion policy after 2020 to cover all European regions, stressing that the policy, which accounts for about one third of EU funds, needs to be strong "so that regions have the resources they need to unite citizens, fight extremism and encourage social and territorial cohesion."
Pointing to the so-called Juncker plan, Rossi said the CPMR supports the policy, which funds projects of strategic importance across Europe, but he said it should not replace cohesion policy, as both policies fulfil different, but complementary, objectives.
Rossi said: "Regions are the link that the EU so desperately needs in these difficult times. Regional authorities are also the pillar of the EU investment policy and act as a bridge between public and private investors. Their value must be recognised and reinforced."