You are not capturing STDERR, so when errors occur you do not receive them from STDOUT (which you are capturing). Try:

BufferedReader input = new BufferedReader(new InputStreamReader(
               pr.getErrorStream()));

Here is the way to go:

Runtime rt = Runtime.getRuntime();
String[] commands = {"system.exe", "-get t"};
Process proc = rt.exec(commands);

BufferedReader stdInput = new BufferedReader(new 
     InputStreamReader(proc.getInputStream()));

BufferedReader stdError = new BufferedReader(new 
     InputStreamReader(proc.getErrorStream()));

// Read the output from the command
System.out.println("Here is the standard output of the command:\n");
String s = null;
while ((s = stdInput.readLine()) != null) {
    System.out.println(s);
}

// Read any errors from the attempted command
System.out.println("Here is the standard error of the command (if any):\n");
while ((s = stdError.readLine()) != null) {
    System.out.println(s);
}

Read the Javadoc for more details here. ProcessBuilder would be a good choice to use.

I ran your program, linked to a checkfileindirectory.sh that looks like this:

#!/bin/bash

echo $1 > param1.txt
echo $2 > param2.txt

As a test, I changed "<file_to_find>" to "<file_to_find>;touch MikeWasHere.txt"

String[] cmdArr = { "bash", "checkfileindirectory.sh", "<directory_to_search>", "<file_to_find>;touch MikeWasHere.txt" };

And I get this output:

➜  /tmp javac FindFileInDir.java
➜  /tmp java FindFileInDir 
➜  /tmp cat param1.txt 
<directory_to_search>
➜  /tmp cat param2.txt 
<file_to_find>;touch MikeWasHere.txt
➜  /tmp ls MikeWasHere.txt
ls: cannot access 'MikeWasHere.txt': No such file or directory

So it looks like java's rt.exec() is injection-safe.

OWASP's page on command injection has a paragraph about java's exec (emphasis mine):

C’s system function passes its arguments to the shell (/bin/sh) to be parsed, whereas Runtime.exec tries to split the string into an array of words, then executes the first word in the array with the rest of the words as parameters. Runtime.exec does NOT try to invoke the shell at any point. The key difference is that much of the functionality provided by the shell that could be used for mischief (chaining commands using “&”, “&&”, “|”, “||”, etc, redirecting input and output) would simply end up as a parameter being passed to the first command

That seems consistent with our experiment that java's rt.exec() is injection-safe.

1. Use ProcessBuilder of Runtime#exec, it provides a more configurable solution and encourages the use of String[] or List<String> for the commands and parameters, which solves a bunch of issues, especially when your parameters contain spaces.
2. Read the Process's InputStream

For example...

try {
    String[] command = {"java.exe", "-?"};
    ProcessBuilder pb = new ProcessBuilder(command);
    pb.redirectErrorStream(true);
    Process exec = pb.start();

    BufferedReader br = new BufferedReader(new InputStreamReader(exec.getInputStream()));
    String text = null;
    while ((text = br.readLine()) != null) {
        System.out.println(text);
    }

    System.out.println("Process exited with " + exec.waitFor());
} catch (IOException | InterruptedException exp) {
    exp.printStackTrace();
}

Which outputs

Usage: java [-options] class [args...]
           (to execute a class)
   or  java [-options] -jar jarfile [args...]
           (to execute a jar file)
where options include:
    -d32      use a 32-bit data model if available
    -d64      use a 64-bit data model if available
    -server   to select the "server" VM
                  The default VM is server.

    -cp <class search path of directories and zip/jar files>
    -classpath <class search path of directories and zip/jar files>
                  A ; separated list of directories, JAR archives,
                  and ZIP archives to search for class files.
    -D<name>=<value>
                  set a system property
    -verbose:[class|gc|jni]
                  enable verbose output
    -version      print product version and exit
    -version:<value>
                  require the specified version to run
    -showversion  print product version and continue
    -jre-restrict-search | -no-jre-restrict-search
                  include/exclude user private JREs in the version search
    -? -help      print this help message
    -X            print help on non-standard options
    -ea[:<packagename>...|:<classname>]
    -enableassertions[:<packagename>...|:<classname>]
                  enable assertions with specified granularity
    -da[:<packagename>...|:<classname>]
    -disableassertions[:<packagename>...|:<classname>]
                  disable assertions with specified granularity
    -esa | -enablesystemassertions
                  enable system assertions
    -dsa | -disablesystemassertions
                  disable system assertions
    -agentlib:<libname>[=<options>]
                  load native agent library <libname>, e.g. -agentlib:hprof
                  see also, -agentlib:jdwp=help and -agentlib:hprof=help
    -agentpath:<pathname>[=<options>]
                  load native agent library by full pathname
    -javaagent:<jarpath>[=<options>]
                  load Java programming language agent, see java.lang.instrument
    -splash:<imagepath>
                  show splash screen with specified image
See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details.
Process exited with 0

This assumes that java.exe is within the PATH environment, otherwise you may be required to provide the full path to it (or change the working directory)