Skeletal oxygen isotope ratios in Holocene Porites corals from northern Papua New Guinea record decreases in sea surface temperature (SST) and rainfall during El Niño events. Threshold analysis of seven fossil coral δ18O records spanning the period 7.6–5.4 ka (thousand years ago) shows 8–12 El Niño events/century, significantly less than the 23 events/century recorded by the NINO3.4 Index. The coral reconstructions also show a 15% reduction in El Niño event amplitude for 7.6–5.4 ka, compared to today, which is greater than the suppression given by model studies. In contrast, large and protracted El Niño events are identified for 2.5–1.7 ka. Taken together, the results indicate a non-linear atmospheric response to Holocene changes in El Niño SST anomalies. We propose that small changes in tropical SST gradients, the positioning of the Intertropical Convergence Zone, and the Pacific tradewind climatology modify the impact of El Niño events on western Pacific rainfall.