diff --git a/src/opm/output/eclipse/WriteInit.cpp b/src/opm/output/eclipse/WriteInit.cpp
index dc45f92b0..3ce65a312 100644
--- a/src/opm/output/eclipse/WriteInit.cpp
+++ b/src/opm/output/eclipse/WriteInit.cpp
@@ -24,6 +24,8 @@
 
 #include <opm/output/eclipse/WriteInit.hpp>
 
+#include <opm/common/OpmLog/OpmLog.hpp>
+
 #include <opm/io/eclipse/OutputStream.hpp>
 
 #include <opm/output/data/Solution.hpp>
@@ -541,16 +543,34 @@ namespace {
                              const ::Opm::UnitSystem&          units,
                              ::Opm::EclIO::OutputStream::Init& initFile)
     {
+        const auto& ph = es.runspec().phases();
+
         const auto epsVectors = ScalingVectors{}
             .withHysteresis(es.runspec().hysterPar().active())
-            .collect       (es.runspec().phases());
+            .collect       (ph);
+
+        const auto nactph = ph.active(::Opm::Phase::WATER)
+            + ph.active(Opm::Phase::OIL)
+            + ph.active(Opm::Phase::GAS);
 
         const auto& props = es.get3DProperties().getDoubleProperties();
 
-        if (! es.cfg().init().filleps()) {
-            // No FILLEPS in input deck.  Output those endpoint arrays that
-            // exist in the input deck.  Write sentinel value if input
-            // defaulted.
+        if (! es.cfg().init().filleps() || (nactph < 3)) {
+            if (nactph < 3) {
+                const auto msg = "OPM-Flow does currently not support "
+                    "FILLEPS for fewer than 3 active phases. "
+                    "Ignoring FILLEPS for "
+                    + std::to_string(nactph)
+                    + " active phases.";
+
+                Opm::OpmLog::warning(msg);
+            }
+
+            // No FILLEPS in input deck or number of active phases
+            // unsupported by Flow's saturation function finalizers.
+            //
+            // Output only those endpoint arrays that exist in the input
+            // deck.  Write sentinel value if input defaulted.
             writeDoubleCellProperties(epsVectors.getVectors(), props,
                                       grid, units, true, initFile);
         }