Background Two epidemiologically-unrelated clusters of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae were detected among several healthcare facilities (HCF) in Finland by routine surveillance using whole genome sequencing (WGS). Aim The objective was to investigate transmission chains to stop further spread of the responsible strain. Methods In this observational retrospective study, cases were defined as patients with K. pneumoniae KPC-3 sequence type (ST)512 strain detected in Finland from August 2013 to May 2018. Environmental specimens were obtained from surfaces, sinks and toilets in affected wards. WGS was performed on K. pneumoniae cultures using Illumina MiSeq platform and data were analysed using Ridom SeqShere software K. pneumoniae core genome multilocus sequence typing (cgMLST) scheme. Epidemiological information of the cases was provided by HCFs. Results We identified 20 cases in six HCFs: cluster 1 included 18 cases in five HCFs and cluster 2 two cases in one HCF. In cluster 1, a link with a foreign country was unclear, 6/18 cases without overlapping stay had occupied the same room in one of the five HCFs within > 3 years. In cluster 2, the index case was transferred from abroad, both cases occupied the same room 8 months apart. A strain identical to that of the two cases in cgMLST was isolated from the toilet of the room, suggesting a clonal origin. Conclusions The clusters were mostly related to case transfer between facilities and likely involved environmental transmission. We show that CPE surveillance using WGS and collaboration between hospitals are crucial to identify clusters and trace transmission chains.