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Background  With the documentation of cases of  falciparum  malaria negative by rapid diagnostic tests (RDT), though at low frequency from natural isolates in a small pocket of Odisha, it became absolutely necessary to investigate the status of HRP-2 based RDT throughout the state and in different seasons of the year.    Methods  Suspected individuals were screened for malaria infection by microscopy and RDT in 25/30 districts of Odisha, India. Discrepancies in results were confirmed by PCR. False negative RDT samples for  Plasmodium falciparum  mono-infection were evaluated for detection of HRP2 antigen in ELISA and genotyped for  pfhrp2 ,  pfhrp3  and their flanking genes. Multiplicity of infection was ascertained based on  msp1  and  msp2  genotyping and parasitaemia level was determined by microscopy.    Results  Of the total 1058 patients suspected for malaria, 384 were microscopically confirmed for  P. falciparum  mono-infection and RDT failure was observed in 58 samples at varying proportion in different regions of the state. The failure in detection was due to undetectable level of HRP-2. Although most of these samples were screened during rainy season (45/345), significantly high proportion (9/17) of RDT negative samples were obtained during the summer compared to rainy season (P = 0.0002; OR = 7.5). PCR genotyping of  pfhrp2  and  pfhrp3  in RDT negative samples showed 38/58 (65.5) samples to be  pfhrp2  negative and 24/58 (41.4) to be  pfhrp3  negative including dual negative in 17/58 (29.3). Most of the RDT negative samples (39/58) were with single genotype infection and high proportions of  pfhrp2  deletion (7/9) was observed in summer. No difference in parasitaemia level was observed between RDT positive and RDT negative patients.    Conclusion  High prevalence of parasites with  pfhrp2  deletion including dual deletions ( pfhrp2  and  pfhrp3 ) is a serious cause of concern, as these patients could not be given a correct diagnosis and treatment. Therefore, HRP2-based RDT for diagnosing  P. falciparum  infection in Odisha is non-reliable and must be performed in addition to or replaced by other appropriate diagnostic tools for clinical management of the disease.    Electronic supplementary material  The online version of this article (10.1186/s12936-018-2502-3) contains supplementary material, which is available to authorized users.

High proportions of pfhrp2 gene deletion and performance of HRP2-based rapid diagnostic test in Plasmodium falciparum field isolates of Odisha