We consider the finite exceptional group of Lie type G=E6ε(q) (universal version) with 3|q−ε, where E6+1(q)=E6(q) and E6−1(q)=2E6(q). We classify, up to conjugacy, all maximal-proper 3-local subgroups of G, that is, all 3-local M<G which are maximal with respect to inclusion among all proper subgroups of G which are 3-local. To this end, we also determine, up to conjugacy, all elementary-abelian 3-subgroups containing Z(G), all extraspecial subgroups containing Z(G), and all cyclic groups of order 9 containing Z(G). These classifications are an important first step towards a classification of the 3-radical subgroups of G, which play a crucial role in many open conjectures in modular representation theory.