In this paper we consider the numerical solution of discrete boundary integral equations on polyhedral surfaces in three dimensions. When the solution contains typical edge singularities, highly stretched meshes are preferred to uniform meshes, since they reduce the number of degrees of freedom needed to obtain a fixed accuracy. The classical panel-clustering method can still be applied in the presence of such highly stretched meshes. However, we will show that the savings in computation time and storage become suboptimal because the near field matrix arising in the panel-clustering algorithm is no longer as sparse as it is in the case of uniform meshes. Hence, a natural question arises as to whether a new enhanced panel-clustering algorithm can be designed which performs efficiently even in the presence of highly stretched meshes. The main result of this paper is to formulate such an enhanced version of the panel-clustering algorithm. The key features of the algorithm are (i) the employment of partial analytic integration in the direction of stretching, yielding a new kernel function on a one-dimensional manifold where the influence of high aspect ratios in the stretched elements is removed, and (ii) the introduction of a generalized admissibility condition with respect to the partially integrated kernel, which ensures that certain stretched clusters which are inadmissible in the classical sense now become admissible. In the context of a model problem, we prove that our algorithm yields an accurate (up to the discretization error) matrix-vector multiplication which requires O(Nlog(k)N) operations, where N is the number of degrees of freedom and k is small and independent of the aspect ratio. The generalized admissibility condition can be viewed as an addition to the classical method which may be useful in general when stretched meshes are present. We also have performed a numerical experiment which shows that the sparsity of the near field matrix for the enhanced panel-clustering method is not negatively affected by stretched elements, and the method will perform optimally.