diff --git a/snakemake/deployment/conda.py b/snakemake/deployment/conda.py
index 473ac2b23..d409e6952 100644
--- a/snakemake/deployment/conda.py
+++ b/snakemake/deployment/conda.py
@@ -624,19 +624,16 @@ def _check(self):
         try:
             version = shell.check_output(
                 self._get_cmd("conda --version"),
-                stderr=subprocess.STDOUT,
+                stderr=subprocess.PIPE,
                 universal_newlines=True,
             )
-            if self.container_img:
-                version = "\n".join(
-                    filter(
-                        lambda line: not line.startswith("WARNING:")
-                        and not line.startswith("ERROR:"),
-                        version.splitlines(),
-                    )
+            version_matches = re.findall("\d+.\d+.\d+", version)
+            if len(version_matches) != 1:
+                raise WorkflowError(
+                    f"Unable to determine conda version. 'conda --version' returned {version}"
                 )
-
-            version = version.split()[1]
+            else:
+                version = version_matches[0]
             if StrictVersion(version) < StrictVersion("4.2"):
                 raise CreateCondaEnvironmentException(
                     "Conda must be version 4.2 or later, found version {}.".format(
@@ -645,7 +642,7 @@ def _check(self):
                 )
         except subprocess.CalledProcessError as e:
             raise CreateCondaEnvironmentException(
-                "Unable to check conda version:\n" + e.output.decode()
+                "Unable to check conda version:\n" + e.stderr.decode()
             )
 
     def bin_path(self):